From 0ac31e861af0edfe67c1b82d086298b2d9fc9081 Mon Sep 17 00:00:00 2001 From: ericblanc20 Date: Tue, 4 Jul 2023 15:57:28 +0200 Subject: [PATCH 01/19] feat: 385 cbioportal export wrapper missing information (#411) --- .../workflows/cbioportal_export/Snakefile | 228 ++--- .../workflows/cbioportal_export/__init__.py | 888 ++++++++++++------ .../workflows/ngs_mapping/Snakefile | 47 + .../workflows/ngs_mapping/__init__.py | 107 +++ .../__init__.py | 45 +- .../cnvkit.rules | 17 + .../somatic_wgs_cnv_calling/__init__.py | 53 +- .../somatic_wgs_cnv_calling/cnvkit.rules | 16 + .../wrappers/cbioportal/case_lists/wrapper.py | 36 +- .../cbioportal/clinical_data/wrapper.py | 88 +- .../compute_signatures/environment.yaml | 9 - .../cbioportal/compute_signatures/wrapper.py | 82 -- .../cbioportal/generate_cna/environment.yaml | 14 + .../wrappers/cbioportal/generate_cna/script.R | 32 + .../cbioportal/generate_cna/wrapper.py | 62 ++ .../wrappers/cbioportal/helper_functions.R | 408 ++++++++ .../cbioportal/merge_tables/environment.yaml | 15 +- .../wrappers/cbioportal/merge_tables/script.R | 162 ++++ .../cbioportal/merge_tables/wrapper.py | 81 +- .../meta_files/meta_clinical_patient.txt | 4 +- .../meta_files/meta_clinical_sample.txt | 4 +- ...eta_CNA_gistic.txt => meta_cna_gistic.txt} | 4 +- .../{meta_CNA_log2.txt => meta_cna_log2.txt} | 4 +- .../cbioportal/meta_files/meta_expression.txt | 8 + .../meta_files/meta_expression_zscores.txt | 8 - .../meta_files/meta_mutation_extended.txt | 2 +- .../cbioportal/meta_files/meta_segment.txt | 4 +- .../cbioportal/meta_files/meta_study.txt | 7 + .../wrappers/cbioportal/meta_files/wrapper.py | 13 +- .../environment.yaml | 9 - .../plot_expression_distribution/wrapper.py | 77 -- .../rank_expression/environment.yaml | 12 - .../cbioportal/rank_expression/wrapper.py | 76 -- .../rpkm_expression/environment.yaml | 12 - .../cbioportal/rpkm_expression/scripts.R | 1 - .../cbioportal/rpkm_expression/wrapper.py | 50 - snappy_wrappers/wrappers/cbioportal/scripts.R | 496 ---------- .../cbioportal/study_meta/environment.yaml | 1 - .../wrappers/cbioportal/study_meta/wrapper.py | 28 - .../cbioportal/zscores/environment.yaml | 11 - .../wrappers/cbioportal/zscores/scripts.R | 1 - .../cbioportal/zscores/snappy-run-zscores.R | 376 -------- .../wrappers/cbioportal/zscores/wrapper.py | 57 -- .../cnvkit/postprocess/environment.yaml | 7 + .../wrappers/cnvkit/postprocess/wrapper.py | 82 ++ snappy_wrappers/wrappers/rseqc/wrapper.py | 146 ++- .../wrappers/vcf2maf/vcf_to_table/action.py | 10 + .../vcf2maf/vcf_to_table/annotation.py | 166 ++++ .../vcf2maf/vcf_to_table/common_functions.py | 119 +++ .../wrappers/vcf2maf/vcf_to_table/config.yaml | 781 +++++++++++++++ .../vcf2maf/vcf_to_table/environment.yaml | 7 + .../vcf2maf/vcf_to_table/exceptions.py | 22 + .../vcf2maf/vcf_to_table/functions.py | 161 ++++ .../wrappers/vcf2maf/vcf_to_table/parser.py | 427 +++++++++ .../vcf_to_table/protein_mutation_parser.py | 433 +++++++++ .../vcf_to_table/variant_classification.py | 125 +++ .../vcf2maf/vcf_to_table/vcf_to_table.py | 421 +++++++++ .../wrappers/vcf2maf/vcf_to_table/wrapper.py | 57 ++ .../test_workflows_cbioportal_export.py | 644 +++++++------ .../workflows/test_workflows_ngs_mapping.py | 1 + ...t_workflows_ngs_mapping_processed_fastq.py | 113 ++- ...kflows_somatic_targeted_seq_cnv_calling.py | 59 +- .../test_workflows_somatic_wgs_cnv_calling.py | 53 +- 63 files changed, 5369 insertions(+), 2120 deletions(-) delete mode 100644 snappy_wrappers/wrappers/cbioportal/compute_signatures/environment.yaml delete mode 100644 snappy_wrappers/wrappers/cbioportal/compute_signatures/wrapper.py create mode 100644 snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml create mode 100644 snappy_wrappers/wrappers/cbioportal/generate_cna/script.R create mode 100644 snappy_wrappers/wrappers/cbioportal/generate_cna/wrapper.py create mode 100644 snappy_wrappers/wrappers/cbioportal/helper_functions.R create mode 100644 snappy_wrappers/wrappers/cbioportal/merge_tables/script.R rename snappy_wrappers/wrappers/cbioportal/meta_files/{meta_CNA_gistic.txt => meta_cna_gistic.txt} (79%) rename snappy_wrappers/wrappers/cbioportal/meta_files/{meta_CNA_log2.txt => meta_cna_log2.txt} (71%) create mode 100644 snappy_wrappers/wrappers/cbioportal/meta_files/meta_expression.txt delete mode 100644 snappy_wrappers/wrappers/cbioportal/meta_files/meta_expression_zscores.txt create mode 100644 snappy_wrappers/wrappers/cbioportal/meta_files/meta_study.txt delete mode 100644 snappy_wrappers/wrappers/cbioportal/plot_expression_distribution/environment.yaml delete mode 100644 snappy_wrappers/wrappers/cbioportal/plot_expression_distribution/wrapper.py delete mode 100644 snappy_wrappers/wrappers/cbioportal/rank_expression/environment.yaml delete mode 100644 snappy_wrappers/wrappers/cbioportal/rank_expression/wrapper.py delete mode 100644 snappy_wrappers/wrappers/cbioportal/rpkm_expression/environment.yaml delete mode 120000 snappy_wrappers/wrappers/cbioportal/rpkm_expression/scripts.R delete mode 100644 snappy_wrappers/wrappers/cbioportal/rpkm_expression/wrapper.py delete mode 100644 snappy_wrappers/wrappers/cbioportal/scripts.R delete mode 100644 snappy_wrappers/wrappers/cbioportal/study_meta/environment.yaml delete mode 100644 snappy_wrappers/wrappers/cbioportal/study_meta/wrapper.py delete mode 100644 snappy_wrappers/wrappers/cbioportal/zscores/environment.yaml delete mode 120000 snappy_wrappers/wrappers/cbioportal/zscores/scripts.R delete mode 100644 snappy_wrappers/wrappers/cbioportal/zscores/snappy-run-zscores.R delete mode 100644 snappy_wrappers/wrappers/cbioportal/zscores/wrapper.py create mode 100644 snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml create mode 100644 snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/action.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/annotation.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/common_functions.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/config.yaml create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/exceptions.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/functions.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/parser.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/variant_classification.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/vcf_to_table.py create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py diff --git a/snappy_pipeline/workflows/cbioportal_export/Snakefile b/snappy_pipeline/workflows/cbioportal_export/Snakefile index 64124553d..66878c620 100644 --- a/snappy_pipeline/workflows/cbioportal_export/Snakefile +++ b/snappy_pipeline/workflows/cbioportal_export/Snakefile @@ -1,6 +1,7 @@ # -*- coding: utf-8 -*- """CUBI Pipeline cbioportal_export step Snakefile""" +import csv import os from snappy_pipeline import expand_ref @@ -28,8 +29,13 @@ exclude_flag = wf.w_config["step_config"]["cbioportal_export"]["exclude_variant_ localrules: - # Linking files from work/ to output/ should be done locally - cbioportal_export_link_out_run, + # Assembling meta files & concatenating results should be done locally + # The sub steps requiring R for merging (CNA) *CANNOT* be done locally + # Neither the expression sub-step (computation of RPKM) + cbioportal_export_meta_files, + cbioportal_export_patient_data, + cbioportal_export_case_lists, + cbioportal_export_concatenate_maf, rule all: @@ -37,63 +43,24 @@ rule all: wf.get_result_files(), -# House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -# Generic linking out --------------------------------------------------------- - - -rule cbioportal_export_link_out_run: - input: - wf.get_input_files("link_out", "run"), - output: - wf.get_output_files("link_out", "run"), - run: - shell(wf.get_shell_cmd("link_out", "run", wildcards)) - - # cbioportal study metadata ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -rule cbioportal_export_study_metadata: - output: - meta_file="work/upload/meta_study.txt", - threads: wf.get_resource("cbioportal_study_meta_files", "run", "threads") - resources: - time=wf.get_resource("cbioportal_study_meta_files", "run", "time"), - memory=wf.get_resource("cbioportal_study_meta_files", "run", "memory"), - partition=wf.get_resource("cbioportal_study_meta_files", "run", "partition"), - tmpdir=wf.get_resource("cbioportal_study_meta_files", "run", "tmpdir"), - wrapper: - wf.wrapper_path("cbioportal/study_meta") - - rule cbioportal_export_meta_files: output: wf.get_output_files("cbioportal_meta_files", "run"), - threads: wf.get_resource("cbioportal_meta_files", "run", "threads") - resources: - time=wf.get_resource("cbioportal_meta_files", "run", "time"), - memory=wf.get_resource("cbioportal_meta_files", "run", "memory"), - partition=wf.get_resource("cbioportal_meta_files", "run", "partition"), - tmpdir=wf.get_resource("cbioportal_meta_files", "run", "tmpdir"), wrapper: wf.wrapper_path("cbioportal/meta_files") -# cbioportal patient and sample metadata ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +# cbioportal patient and sample data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -rule cbioportal_export_patient_metadata: +rule cbioportal_export_patient_data: output: **wf.get_output_files("cbioportal_clinical_data", "run"), - threads: wf.get_resource("cbioportal_clinical_data", "run", "threads") - resources: - time=wf.get_resource("cbioportal_clinical_data", "run", "time"), - memory=wf.get_resource("cbioportal_clinical_data", "run", "memory"), - partition=wf.get_resource("cbioportal_clinical_data", "run", "partition"), - tmpdir=wf.get_resource("cbioportal_clinical_data", "run", "tmpdir"), params: - sheet=wf.substep_dispatch("cbioportal_clinical_data", "get_sample_sheets", "run"), + **wf.get_args("cbioportal_clinical_data", "run"), wrapper: wf.wrapper_path("cbioportal/clinical_data") @@ -101,19 +68,13 @@ rule cbioportal_export_patient_metadata: rule cbioportal_export_case_lists: output: **wf.get_output_files("cbioportal_case_lists", "run"), - threads: wf.get_resource("cbioportal_case_lists", "run", "threads") - resources: - time=wf.get_resource("cbioportal_case_lists", "run", "time"), - memory=wf.get_resource("cbioportal_case_lists", "run", "memory"), - partition=wf.get_resource("cbioportal_case_lists", "run", "partition"), - tmpdir=wf.get_resource("cbioportal_case_lists", "run", "tmpdir"), params: - sheet=wf.substep_dispatch("cbioportal_clinical_data", "get_sample_sheets", "run"), + **wf.get_args("cbioportal_case_lists", "run"), wrapper: wf.wrapper_path("cbioportal/case_lists") -# cbioportal data preparation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +# Mutation file (data_mutation_extended.txt) ================================== # Create MAF ------------------------------------------------------------------ @@ -130,126 +91,135 @@ rule cbioportal_export_generate_mafs: partition=wf.get_resource("cbioportal_vcf2maf", "run", "partition"), tmpdir=wf.get_resource("cbioportal_vcf2maf", "run", "tmpdir"), params: - args=wf.substep_dispatch("cbioportal_vcf2maf", "get_args", "run"), + args=wf.get_args("cbioportal_vcf2maf", "run"), + log: + **wf.get_log_file("cbioportal_vcf2maf", "run"), wrapper: - wf.wrapper_path("vcf2maf/vcf2maf") + wf.wrapper_path("vcf2maf/vcf_to_table") -# Create one MAF from all MAFs +# Merge all sample MAF files -------------------------------------------------- rule cbioportal_export_concatenate_maf: - # TODO: could this be include in the `localrules`? Or simply incorporated into another step? - # It looks like some postprocessing... input: - *wf.get_input_files("cbioportal_maf", "run"), + **wf.get_input_files("cbioportal_mutations", "run"), output: - "work/upload/data_mutation_extended.txt", - threads: wf.get_resource("cbioportal_maf", "run", "threads") - resources: - time=wf.get_resource("cbioportal_maf", "run", "time"), - memory=wf.get_resource("cbioportal_maf", "run", "memory"), - partition=wf.get_resource("cbioportal_maf", "run", "partition"), - tmpdir=wf.get_resource("cbioportal_maf", "run", "tmpdir"), + wf.get_output_files("cbioportal_mutations", "run"), shell: r""" cat \ - <( head -n2 {input[0]} ) \ - <( tail -q -n +3 {input}) \ - | grep -v {exclude_flag} \ + <( head -n 1 {input[0]} ) \ + <( tail -q -n +2 {input}) \ + | (if [[ -n "{exclude_flag}" ]] ; then grep -v {exclude_flag} ; else cat ; fi) \ > {output} """ -# Create CNA gistic file ------------------------------------------------------ -rule cbioportal_export_CNA_calls: +# Copy number files (data_cna_log2.txt, data_cna_gistic.txt, data_segment.txt) + +# Create CNA files (discrete, continuous from cns files) ---------------------- + + +rule cbioportal_export_generate_cna: input: - wf.get_input_files("cbioportal_cna_data", "gistic"), + **wf.get_input_files("cbioportal_cns2cna", "run"), output: - "work/upload/data_CNA_gistic.txt", - threads: wf.get_resource("cbioportal_cna_data", "gistic", "threads") + **wf.get_output_files("cbioportal_cns2cna", "run"), + threads: wf.get_resource("cbioportal_cns2cna", "run", "threads") resources: - time=wf.get_resource("cbioportal_cna_data", "gistic", "time"), - memory=wf.get_resource("cbioportal_cna_data", "gistic", "memory"), - partition=wf.get_resource("cbioportal_cna_data", "gistic", "partition"), - tmpdir=wf.get_resource("cbioportal_cna_data", "gistic", "tmpdir"), + time=wf.get_resource("cbioportal_cns2cna", "run", "time"), + memory=wf.get_resource("cbioportal_cns2cna", "run", "memory"), + partition=wf.get_resource("cbioportal_cns2cna", "run", "partition"), + tmpdir=wf.get_resource("cbioportal_cns2cna", "run", "tmpdir"), params: - datatype="int", + **wf.get_args("cbioportal_cns2cna", "run"), + log: + **wf.get_log_file("cbioportal_cns2cna", "run"), wrapper: - wf.wrapper_path("cbioportal/merge_tables") + wf.wrapper_path("cbioportal/generate_cna") -# Create CNA log2 file -------------------------------------------------------- +# Merge sample-based CNA files to cBioPortal ---------------------------------- -rule cbioportal_export_CNA_log2: +rule cbioportal_export_concatenate_cna_log2: input: - wf.get_input_files("cbioportal_cna_data", "log2"), + **wf.get_input_files("cbioportal_cna", "log2"), output: - "work/upload/data_CNA_log2.txt", - threads: wf.get_resource("cbioportal_cna_data", "log2", "threads") - resources: - time=wf.get_resource("cbioportal_cna_data", "log2", "time"), - memory=wf.get_resource("cbioportal_cna_data", "log2", "memory"), - partition=wf.get_resource("cbioportal_cna_data", "log2", "partition"), - tmpdir=wf.get_resource("cbioportal_cna_data", "log2", "tmpdir"), + wf.get_output_files("cbioportal_cna", "log2"), params: - datatype="float", + **wf.get_args("cbioportal_cna", "log2"), + threads: wf.get_resource("cbioportal_cna", "log2", "threads") + resources: + time=wf.get_resource("cbioportal_cna", "log2", "time"), + memory=wf.get_resource("cbioportal_cna", "log2", "memory"), + partition=wf.get_resource("cbioportal_cna", "log2", "partition"), + tmpdir=wf.get_resource("cbioportal_cna", "log2", "tmpdir"), + log: + **wf.get_log_file("cbioportal_cna", "log2"), wrapper: wf.wrapper_path("cbioportal/merge_tables") -# Create CNA segmentation file ------------------------------------------------ - - -rule cbioportal_export_segments: +rule cbioportal_export_concatenate_cna_gistic: input: - wf.get_input_files("cbioportal_cna_data", "segments"), + **wf.get_input_files("cbioportal_cna", "gistic"), output: - "work/upload/data_segment.txt", - threads: wf.get_resource("cbioportal_cna_data", "segments", "threads") + wf.get_output_files("cbioportal_cna", "gistic"), + params: + **wf.get_args("cbioportal_cna", "gistic"), + threads: wf.get_resource("cbioportal_cna", "gistic", "threads") resources: - time=wf.get_resource("cbioportal_cna_data", "segments", "time"), - memory=wf.get_resource("cbioportal_cna_data", "segments", "memory"), - partition=wf.get_resource("cbioportal_cna_data", "segments", "partition"), - tmpdir=wf.get_resource("cbioportal_cna_data", "segments", "tmpdir"), - shell: - r""" - cat \ - <( head -n1 {input[0]} ) \ - <( tail -q -n +2 {input}) \ - | sed 's/-DNA.-W[EG]S.//' \ - > {output} - """ + time=wf.get_resource("cbioportal_cna", "gistic", "time"), + memory=wf.get_resource("cbioportal_cna", "gistic", "memory"), + partition=wf.get_resource("cbioportal_cna", "gistic", "partition"), + tmpdir=wf.get_resource("cbioportal_cna", "gistic", "tmpdir"), + log: + **wf.get_log_file("cbioportal_cna", "gistic"), + wrapper: + wf.wrapper_path("cbioportal/merge_tables") -# Create expression z-scores -------------------------------------------------- +# Merge sample-based segment files to cBioPortal ------------------------------ -rule cbioportal_create_dataframe_matching_results: - # TODO: could this be include in the `localrules`? +rule cbioportal_export_concatenate_segments: + input: + **wf.get_input_files("cbioportal_segment", "run"), output: - "work/zscores_mapping_df.tsv", - threads: wf.get_resource("cbioportal_zscores", "run", "threads") + wf.get_output_files("cbioportal_segment", "run"), + params: + action_type="segment", + threads: wf.get_resource("cbioportal_segment", "run", "threads") resources: - time=wf.get_resource("cbioportal_zscores", "run", "time"), - memory=wf.get_resource("cbioportal_zscores", "run", "memory"), - partition=wf.get_resource("cbioportal_zscores", "run", "partition"), - tmpdir=wf.get_resource("cbioportal_zscores", "run", "tmpdir"), - run: - wf.substep_dispatch("cbioportal_zscores", "get_df", output) + time=wf.get_resource("cbioportal_segment", "run", "time"), + memory=wf.get_resource("cbioportal_segment", "run", "memory"), + partition=wf.get_resource("cbioportal_segment", "run", "partition"), + tmpdir=wf.get_resource("cbioportal_segment", "run", "tmpdir"), + log: + **wf.get_log_file("cbioportal_segment", "run"), + wrapper: + wf.wrapper_path("cbioportal/merge_tables") + + +# Create expression RPKMs ----------------------------------------------------- -rule cbioportal_compute_zscores: +rule cbioportal_export_expression: input: - tsv="work/zscores_mapping_df.tsv", + **wf.get_input_files("cbioportal_expression", "run"), output: - tsv="work/upload/data_expression_zscores.txt", - threads: wf.get_resource("cbioportal_compute_zscores", "run", "threads") + wf.get_output_files("cbioportal_expression", "run"), + params: + **wf.get_args("cbioportal_expression", "run"), + threads: wf.get_resource("cbioportal_expression", "run", "threads") resources: - time=wf.get_resource("cbioportal_compute_zscores", "run", "time"), - memory=wf.get_resource("cbioportal_compute_zscores", "run", "memory"), - partition=wf.get_resource("cbioportal_compute_zscores", "run", "partition"), - tmpdir=wf.get_resource("cbioportal_compute_zscores", "run", "tmpdir"), + time=wf.get_resource("cbioportal_expression", "run", "time"), + memory=wf.get_resource("cbioportal_expression", "run", "memory"), + partition=wf.get_resource("cbioportal_expression", "run", "partition"), + tmpdir=wf.get_resource("cbioportal_expression", "run", "tmpdir"), + log: + **wf.get_log_file("cbioportal_expression", "run"), wrapper: - wf.wrapper_path("cbioportal/zscores") + wf.wrapper_path("cbioportal/merge_tables") diff --git a/snappy_pipeline/workflows/cbioportal_export/__init__.py b/snappy_pipeline/workflows/cbioportal_export/__init__.py index 75af96988..e42d917a1 100644 --- a/snappy_pipeline/workflows/cbioportal_export/__init__.py +++ b/snappy_pipeline/workflows/cbioportal_export/__init__.py @@ -11,196 +11,257 @@ """ from collections import OrderedDict -import csv import os import sys from biomedsheets.shortcuts import CancerCaseSheet, CancerCaseSheetOptions, is_not_background -from snakemake.io import expand from snappy_pipeline.base import MissingConfiguration from snappy_pipeline.utils import dictify, listify -from snappy_pipeline.workflows.abstract import ( - BaseStep, - BaseStepPart, - LinkOutStepPart, - ResourceUsage, -) -from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow +from snappy_pipeline.workflows.abstract import BaseStep, BaseStepPart, ResourceUsage # cbioportal meta data files -META_FILES = ( - "meta_clinical_patient.txt", - "meta_clinical_sample.txt", - "meta_CNA_gistic.txt", - "meta_CNA_log2.txt", - "meta_expression_zscores.txt", - "meta_mutation_extended.txt", - "meta_segment.txt", -) +META_FILES = { + "always_present": ["meta_study.txt", "meta_clinical_patient.txt", "meta_clinical_sample.txt"], + "sequenced": ["meta_mutation_extended.txt"], + "cna": ["meta_cna_gistic.txt", "meta_cna_log2.txt"], + "rna_seq_mrna": ["meta_expression.txt"], + "segment": ["meta_segment.txt"], +} # files holding clinical data -CLINICAL_DATA_FILES = ("data_clinical_patients.txt", "data_clinical_samples.txt") +CLINICAL_DATA_FILES = ["data_clinical_patients.txt", "data_clinical_samples.txt"] # files with CNA results -CNA_DATA_FILES = ("data_CNA_gistic.txt", "data_CNA_log2.txt", "data_segment.txt") +CNA_DATA_FILES = ["data_cna_gistic.txt", "data_cna_log2.txt", "data_segment.txt"] + +# case lists files +CASE_LIST_FILES = { + "sequenced": { + "filename": "all_cases_with_mutation_data.txt", + "name": "Sequenced tumors", + "description": "Tumors with somatic variant calls", + "stable_id": "sequenced", + "category": "all_cases_with_mutation_data", + }, + "cna": { + "filename": "all_cases_with_cna_data.txt", + "name": "Tumors with CNA data", + "description": "Tumors with somatic Copy Number Alteration calls", + "stable_id": "cna", + "category": "all_cases_with_cna_data", + }, + "rna_seq_mrna": { + "filename": "all_cases_with_mrna_rnaseq_data.txt", + "name": "Tumors with expression data", + "description": "Tumors with mRNA seq expression data", + "stable_id": "rna_seq_mrna", + "category": "all_cases_with_mrna_rnaseq_data", + }, + "cnaseq": { + "filename": "all_cases_with_mutation_and_cna_data.txt", + "name": "Sequenced tumors with CNA", + "description": "Tumors with somatic variant & CNA calls", + "stable_id": "cnaseq", + "category": "all_cases_with_mutation_and_cna_data", + }, + "3way_complete": { + "filename": "all_cases_with_mutation_and_cna_and_mrna_data.txt", + "name": "Sequenced tumors with CNA & expression", + "description": "Tumors with somatic variant calls, CNA calls & expression data", + "stable_id": "3way_complete", + "category": "all_cases_with_mutation_and_cna_and_mrna_data", + }, +} DEFAULT_CONFIG = r""" step_config: cbioportal_export: - # Paths to snappy steps containing results to be uploaded - path_ngs_mapping: ../ngs_mapping # REQUIRED - path_gene_expression_quantification: ../gene_expression_quantification # Set to '' in absence of mRNA_seq - path_somatic_variant_filtration: ../somatic_variant_filtration # REQUIRED - path_copy_number_step: ../somatic_targeted_seq_cnv_calling # Set to '' for panels, and change for WGS - # Select tools & filter set - cnv_tool: copywriter # Other option: cnvkit, Control_FREEC (unsupported) - tools_somatic_variant_calling: [ "mutect" ] # Possibly scalpel, mutect2, strelka2 - filter_set: dkfz_only # Possibly dkfz_and_ebfilter, dkfz_and_ebfilter_and_oxog, ... - exclude_variant_with_flag: LowFisherScore # REQUIRED - # Additional parameters - vep_data_path: REQUIRED # Variant Effect Predictor DB for vcf -> maf conversion, must match genome release - filter_vcf: REQUIRED # Common germline variants for vcf -> maf conversion, must match genome release - ncbi_build: GRCh37 + # Required for RNA expression + path_ngs_mapping: "" # When missing, no expression data is uploaded to cBioPortal + expression_tool: "star" + # Required for somatic variants + path_somatic_variant: ../somatic_variant_filtration # REQUIRED (before or after filtration) + somatic_variant_calling_tool: "mutect2" # mutect/scalpel combo unsupported + somatic_variant_annotation_tool: "vep" + filter_set: "" # Will take variants before filtration step.dkfz_only. + # For filters, use dkfz_only, dkfz_and_ebfilter, dkfz_and_ebfilter_and_oxog, ... + exon_list: "genome_wide" # Works together with filter set, see somatic_variant_filtration step + exclude_variant_with_flag: "" + # Required for Copy Number Alterations + path_copy_number: "" # When missing, no CNV data uploaded to portal. Access WES & WGS steps + copy_number_tool: cnvkit # Control_FREEC is currently unsupported, CopywriteR is not maintained + # Required for MAF &/or cBioPortal + path_gene_id_mappings: REQUIRED # Mapping from pipeline gene ids to cBioPortal ids (HGNC symbols from GeneNexus) + vcf2maf: + Center: BIH + ncbi_build: GRCh37 # Description of dataset in cBioPortal - type_of_cancer: REQUIRED # REQUIRED - cancer_study_id: REQUIRED # REQUIRED - study_description: REQUIRED # REQUIRED - study_name: REQUIRED # REQUIRED - study_name_short: REQUIRED # REQUIRED - cache_version: 100 - + study: + type_of_cancer: REQUIRED # see http://oncotree.mskcc.org/#/home + cancer_study_id: REQUIRED # Usually: __ + study_description: REQUIRED # REQUIRED + study_name: REQUIRED # REQUIRED + study_name_short: REQUIRED # REQUIRED + patient_info: [] # Unimplemented + sample_info: [] # Each entry must have a path & a step associated, see example below + # - step: tumor_mutational_burden + # path: ../tumor_mutational_burden """ +# ================================================================================================ +# +# Abstract classes: one generic, and the other for substeps dealing with a single sample at a time +# +# ================================================================================================ + + class cbioportalExportStepPart(BaseStepPart): - """Base class for gene expression quantifiers""" + """Base class for all cBioPortal export step parts + + - Builds a mapping between the tumor library id and the normal/tumor sample pair + - Provides a list of input files based on a template, and on the iteration over the sheets. + The template can be changed by derived classes. + """ #: Class available actions - actions = ("run",) + actions = None - def __init__(self, parent): - super().__init__(parent) - # Build shortcut from cancer bio sample name to matched cancer sample - self.tumor_ngs_library_to_sample_pair = OrderedDict() - for sheet in self.parent.shortcut_sheets: - self.tumor_ngs_library_to_sample_pair.update( - sheet.all_sample_pairs_by_tumor_dna_ngs_library - ) + #: Extraction type, must be instantiated in sub-class + extraction_type = None - def iterate_over_biomedsheets(self, action): - """Iterate over biomedsheet, yield input files for cbioportal CNV aggregation - or for z-score computation (only return samples with matched RNA-seq""" - copy_number_step = self.parent.sub_workflows["copy_number_step"] - cnv_tool = self.config["cnv_tool"] - if action == "get_zscores_input": - gene_expression = self.parent.sub_workflows.get("gene_expression_quantification") + #: input files template + input_tpl = None - cnv_tpl = "output/{mapper}.{tool}.{library_name}/out/{mapper}.{tool}.{library_name}_" - exp_tpl = "output/{mapper}.{tool}.{library_name}/out/{mapper}.{tool}.{library_name}.tsv" + #: Output_file name + output_file = None + def _yield_libraries(self): + test_msg = 'WARNING: multiple test samples for sample "{}", test sample "{}" is ignored' + lib_msg = 'WARNING: multiple libraries for sample "{}", library "{}" is ignored' + samples = [] for sheet in filter(is_not_background, self.parent.sheets): for donor in sheet.bio_entities.values(): for biosample in donor.bio_samples.values(): if biosample.extra_infos["isTumor"]: sample_name = biosample.name - rna_library = None - dna_library = None for test_sample in biosample.test_samples.values(): + if ( + self.extraction_type + and test_sample.extra_infos["extractionType"] + != self.extraction_type + ): + continue + if sample_name in samples: + print( + test_msg.format(sample_name, test_sample.name), file=sys.stderr + ) + continue + samples.append(sample_name) + first = True for lib in test_sample.ngs_libraries.values(): - # pick one rna and one dna library - - # even if there is more than one lib, cbioportal cannot use it - if lib.extra_infos["libraryType"] == "mRNA_seq": - rna_library = lib.name - elif lib.extra_infos["libraryType"] == "WES": - dna_library = lib.name - elif lib.extra_infos["libraryType"] == "WGS": - dna_library = lib.name - - # for each tumor sample, format file for DNA and optionally RNA - cnv_file = cnv_tpl.format( - tool=cnv_tool, mapper="bwa", library_name=dna_library - ) - exp_file = None - if rna_library: - exp_file = exp_tpl.format( - tool="featurecounts", mapper="star", library_name=rna_library - ) - - # CNVs - if action == "gistic": - yield copy_number_step(cnv_file + "gene_call.txt") - - elif action == "log2": - yield copy_number_step(cnv_file + "gene_log2.txt") - - elif action == "segments": - yield copy_number_step(cnv_file + "segments.txt") - - # Z scores - elif action == "get_zscores_input" and dna_library and rna_library: - cnv_file_ = copy_number_step(cnv_file + "gene_call.txt") - exp_file_ = gene_expression(exp_file) - yield sample_name, cnv_file_, exp_file_ - - -class CbioportalStudyMetaFilesStepPart(cbioportalExportStepPart): - """Generate cbioportal study meta data files""" - - #: Step name - name = "cbioportal_study_meta_files" + # pick only one library + if not first: + print(lib_msg.format(sample_name, lib.name), file=sys.stderr) + break + yield lib + first = False + @dictify + def get_input_files(self, action): + """Return path of input files for merging""" + # Validate action + self._validate_action(action) + assert self.input_tpl is not None + for lib in self._yield_libraries(): + yield lib.test_sample.bio_sample.name, self.input_tpl.format(library_name=lib.name) -class cbioportalMetaFilesStepPart(cbioportalExportStepPart): - """Generate cbioportal meta data files""" - - #: Step name - name = "cbioportal_meta_files" - - @listify def get_output_files(self, action): # Validate action self._validate_action(action) - yield from [os.path.join("work/upload", f) for f in META_FILES] - - -class cbioportalClinicalDataStepPart(cbioportalExportStepPart): - """Generate cbioportal patient data file""" - - #: Step name - name = "cbioportal_clinical_data" + assert self.output_file is not None + return self.output_file - @dictify - def get_output_files(self, action): + def get_log_file(self, action): + """Return path to log files for all data files""" # Validate action self._validate_action(action) - yield "patients_tsv", os.path.join("work/upload", "data_clinical_patients.txt") - yield "samples_tsv", os.path.join("work/upload", "data_clinical_samples.txt") - def get_sample_sheets(self, action): - sheets = self.parent.sheets - return [sheet for sheet in sheets] + tpl = "work/log/{name}{ext}" + key_ext = ( + ("log", ".log"), + ("conda_info", ".conda_info.txt"), + ("conda_list", ".conda_list.txt"), + ) + log_files = {} + for key, ext in key_ext: + log_files[key] = tpl.format(name=self.name, ext=ext) + log_files[key + "_md5"] = log_files[key] + ".md5" + return log_files -class cbioportalCaseListsStepPart(cbioportalExportStepPart): - """Generate cbioportal patient data file""" +class cbioportalVcf2MafStepPart(BaseStepPart): + """Helper class for VCF2MAF step""" #: Step name - name = "cbioportal_case_lists" + name = "cbioportal_vcf2maf" + + #: Actions + actions = ("run",) + + def __init__(self, parent): + super().__init__(parent) + self.name_pattern = None + if self.config["filter_set"]: + self.name_pattern = ( + "{mapper}.{caller}.{annotator}." + "dkfz_bias_filter.eb_filter.{tumor_library}." + "{filter_set}.{exon_list}" + ) + else: + self.name_pattern = "{mapper}.{caller}.{annotator}.{tumor_library}" + # Build shortcut from cancer bio sample name to matched cancer sample + self.tumor_ngs_library_to_sample_pair = OrderedDict() + for sheet in self.parent.shortcut_sheets: + self.tumor_ngs_library_to_sample_pair.update( + sheet.all_sample_pairs_by_tumor_dna_ngs_library + ) @dictify def get_output_files(self, action): + """Return maf output file""" # Validate action self._validate_action(action) - yield "sequenced", "work/upload/case_lists/all_cases_with_mutation_data.txt" + yield "maf", os.path.join("work/maf", self.name_pattern, "out", self.name_pattern + ".maf") + @dictify + def get_input_files(self, action): + """Return input vcf for each output maf""" + # Validate action + self._validate_action(action) + somatic_variant = self.parent.sub_workflows["somatic_variant"] + tpl = somatic_variant( + os.path.join("output", self.name_pattern, "out", self.name_pattern + ".vcf.gz") + ) + yield "vcf", tpl -class cbioportalVcf2MafStepPart(cbioportalExportStepPart): - """Helper class for VCF2MAF step""" + @dictify + def get_log_file(self, action): + """Return path to log files for all data files""" + # Validate action + self._validate_action(action) - #: Step name - name = "cbioportal_vcf2maf" + tpl = os.path.join("work/maf/", self.name_pattern, "log", self.name_pattern) + key_ext = ( + ("log", ".log"), + ("conda_info", ".conda_info.txt"), + ("conda_list", ".conda_list.txt"), + ) + for key, ext in key_ext: + yield key, tpl + ext + yield key + "_md5", tpl + ext + ".md5" def get_args(self, action): # Validate action @@ -209,53 +270,134 @@ def get_args(self, action): def args_function(wildcards): result = { "tumor_sample": wildcards.tumor_library, - "normal_sample": self.get_normal_lib_name(wildcards), - "tumor_id": self.get_tumor_bio_sample(wildcards), - "normal_id": self.get_normal_bio_sample(wildcards), + "normal_sample": self._get_normal_lib_name(wildcards), + "tumor_id": self._get_tumor_bio_sample(wildcards), + "normal_id": self._get_normal_bio_sample(wildcards), } return result return args_function - def get_normal_lib_name(self, wildcards): + def _get_normal_lib_name(self, wildcards): """Return name of normal (non-cancer) library""" pair = self.tumor_ngs_library_to_sample_pair[wildcards.tumor_library] return pair.normal_sample.dna_ngs_library.name - def get_tumor_bio_sample(self, wildcards): + def _get_tumor_bio_sample(self, wildcards): """Return bio sample to tumor dna ngs library""" - return "-".join(wildcards.tumor_library.split("-")[0:2]) + pair = self.tumor_ngs_library_to_sample_pair[wildcards.tumor_library] + return pair.tumor_sample.dna_ngs_library.test_sample.bio_sample.name - def get_normal_bio_sample(self, wildcards): + def _get_normal_bio_sample(self, wildcards): """Return normal bio sample to tumor dna ngs library""" - normal_lib = self.get_normal_lib_name(wildcards) - return "-".join(normal_lib.split("-")[0:2]) + pair = self.tumor_ngs_library_to_sample_pair[wildcards.tumor_library] + return pair.normal_sample.dna_ngs_library.test_sample.bio_sample.name + + def get_resource_usage(self, action): + """Get Resource Usage + + :param action: Action (i.e., step) in the workflow, example: 'run'. + :type action: str + + :return: Returns ResourceUsage for step. + """ + # Validate action + self._validate_action(action) + return ResourceUsage( + threads=2, + time="02:00:00", # 2 hours + memory="5120M", + ) + + +class cbioportalMutationsStepPart(cbioportalExportStepPart): + """Merges sample MAF files into data_mutation_extended.txt""" + + #: Step name + name = "cbioportal_mutations" + + #: Extraction type, must be instantiated in sub-class + extraction_type = "DNA" + + #: Actions + actions = ("run",) + + #: Output file name + output_file = "work/upload/data_mutation_extended.txt" + + def __init__(self, parent): + super().__init__(parent) + if self.config["filter_set"]: + name_pattern = ( + "{mapper}.{caller}.{annotator}." + "dkfz_bias_filter.eb_filter.{{library_name}}." + "{filter_set}.{exon_list}" + ) + else: + name_pattern = "{mapper}.{caller}.{annotator}.{{library_name}}" + tpl = os.path.join("work/maf", name_pattern, "out", name_pattern + "{ext}") + self.input_tpl = tpl.format( + mapper="bwa", + caller=self.config["somatic_variant_calling_tool"], + annotator=self.config["somatic_variant_annotation_tool"], + filter_set=self.config["filter_set"], + exon_list=self.config["exon_list"], + ext=".maf", + ) + + +class cbioportalCns2CnaStepPart(BaseStepPart): + """Helper class to extract gene-based log2 & copy number call from a cns file""" + + #: Step name + name = "cbioportal_cns2cna" + + #: Actions + actions = ("run",) + + @dictify + def get_input_files(self, action): + """Return the library""" + # Validate action + self._validate_action(action) + name_pattern = "{mapper}.{caller}.{tumor_library}" + yield "cns", os.path.join( + self.config["path_copy_number"], "output", name_pattern, "out", name_pattern + ".cns" + ) @dictify def get_output_files(self, action): """Return maf output file""" # Validate action self._validate_action(action) - name_pattern = ( - "{mapper}.{caller}.jannovar_annotate_somatic_vcf." - "dkfz_bias_filter.eb_filter.{tumor_library}." - "{filter_set}.{exon_list}" - ) - yield "maf", os.path.join("work/maf", name_pattern, "out", name_pattern + ".maf") + name_pattern = "{mapper}.{caller}.{tumor_library}" + yield "cna", os.path.join("work/cna", name_pattern, "out", name_pattern + ".cna") @dictify - def get_input_files(self, action): - """Return input vcf for each output maf""" + def get_log_file(self, action): + """Return path to log files for all data files""" # Validate action self._validate_action(action) - name_pattern = ( - "{mapper}.{caller}.jannovar_annotate_somatic_vcf." - "dkfz_bias_filter.eb_filter.{tumor_library}." - "{filter_set}.{exon_list}" + name_pattern = "{mapper}.{caller}.{tumor_library}" + tpl = os.path.join("work/cna/", name_pattern, "log", name_pattern) + key_ext = ( + ("log", ".log"), + ("conda_info", ".conda_info.txt"), + ("conda_list", ".conda_list.txt"), ) - tpl = (os.path.join("output", name_pattern, "out", name_pattern + ".vcf.gz"),) - somatic_variant_filtration = self.parent.sub_workflows["somatic_variant_filtration"] - yield "vcf", somatic_variant_filtration(tpl) + for key, ext in key_ext: + yield key, tpl + ext + yield key + "_md5", tpl + ext + ".md5" + + def get_args(self, action): + # Validate action + self._validate_action(action) + return { + "features": self.parent.w_config["step_config"]["ngs_mapping"][ + self.config["expression_tool"] + ]["path_features"], + "pipeline_id": "ENSEMBL", + } def get_resource_usage(self, action): """Get Resource Usage @@ -268,77 +410,141 @@ def get_resource_usage(self, action): # Validate action self._validate_action(action) return ResourceUsage( - threads=4, - time="12:00:00", # 12 hours - memory="5120M", + threads=2, + time="02:00:00", # 2 hours + memory="8192M", ) -class cbioportalMafStepPart(cbioportalExportStepPart): - """Helper class to get all required maf files for cbioportal.""" +class cbioportalCnaFilesStepPart(cbioportalExportStepPart): + """Generate cbioportal continuous (log2), discrete (pseudo-gistic) & segment tables""" #: Step name - name = "cbioportal_maf" + name = "cbioportal_cna" - @listify - def get_input_files(self, action): - """Return list of all input files""" + #: Extraction type, must be instantiated in sub-class + extraction_type = "DNA" + + #: Actions + actions = ("log2", "gistic") + + def __init__(self, parent): + super().__init__(parent) + name_pattern = "bwa." + self.config["copy_number_tool"] + ".{library_name}" + self.input_tpl = os.path.join("work/cna", name_pattern, "out", name_pattern + ".cna") + + def get_args(self, action): + # Validate action + self._validate_action(action) + if action == "gistic": + return {"action_type": "gistic", "extra_args": {"pipeline_id": "ENSEMBL"}} + if action == "log2": + return { + "action_type": "log2", + "extra_args": { + "pipeline_id": "ENSEMBL", + "amplification": "9", + }, # Amplification: cn >= 9 (https://doi.org/10.1038/s41586-022-04738-6) + } + + def get_output_files(self, action): + # Validate action + self._validate_action(action) + return "work/upload/data_cna_{action}.txt".format(action=action) + + def get_resource_usage(self, action): + """Get Resource Usage + + :param action: Action (i.e., step) in the workflow, example: 'run'. + :type action: str + + :return: Returns ResourceUsage for step. + """ # Validate action self._validate_action(action) - name_pattern = ( - "{mapper}.{caller}.jannovar_annotate_somatic_vcf." - "dkfz_bias_filter.eb_filter.{tumor_library}." - "{filter_set}.{exon_list}" + return ResourceUsage( + threads=2, + time="02:00:00", # 2 hours + memory="8192M", ) - filter_sets = self.config["filter_set"] - exon_lists = ["genome_wide"] - callers = set(self.config["tools_somatic_variant_calling"]) - yield from self._yield_result_files_matched( - os.path.join("work/maf", name_pattern, "out", name_pattern + "{ext}"), - mapper="bwa", - caller=callers, - filter_set=filter_sets, - exon_list=exon_lists, - ext=".maf", + + +class cbioportalSegmentStepPart(cbioportalExportStepPart): + + #: Step name + name = "cbioportal_segment" + + #: Extraction type, must be instantiated in sub-class + extraction_type = "DNA" + + #: Actions + actions = ("run",) + + #: Output file name + output_file = "work/upload/data_segment.txt" + + def __init__(self, parent): + super().__init__(parent) + name_pattern = "bwa." + self.config["copy_number_tool"] + ".{library_name}" + self.input_tpl = os.path.join( + self.config["path_copy_number"], "output", name_pattern, "out", name_pattern + ".cns" ) - def _yield_result_files_matched(self, tpl, **kwargs): - """Build output paths from path template and extension list. + def get_resource_usage(self, action): + """Get Resource Usage + + :param action: Action (i.e., step) in the workflow, example: 'run'. + :type action: str - This function returns the results from the matched somatic variant callers such as - Mutect. + :return: Returns ResourceUsage for step. """ - for sheet in filter(is_not_background, self.parent.shortcut_sheets): - for sample_pair in sheet.all_sample_pairs: - if ( - not sample_pair.tumor_sample.dna_ngs_library - or not sample_pair.normal_sample.dna_ngs_library - ): - msg = ( - "INFO: sample pair for cancer bio sample {} has is missing primary" - "normal or primary cancer NGS library" - ) - print(msg.format(sample_pair.tumor_sample.name), file=sys.stderr) - continue - yield from expand( - tpl, tumor_library=[sample_pair.tumor_sample.dna_ngs_library.name], **kwargs - ) + # Validate action + self._validate_action(action) + return ResourceUsage( + threads=2, + time="02:00:00", # 2 hours + memory="8192M", + ) -class cbioportalCnaFilesStepPart(cbioportalExportStepPart): - """Generate cbioportal cna data files""" +class cbioportalExpressionStepPart(cbioportalExportStepPart): + """Generates the expression table (z-scores or FPKM)""" #: Step name - name = "cbioportal_cna_data" + name = "cbioportal_expression" - #: Class available actions - actions = ("log2", "gistic", "segments") + #: Extraction type, must be instantiated in sub-class + extraction_type = "RNA" - @listify - def get_input_files(self, action): + #: Action + actions = ("run",) + + #: Output file name + output_file = "work/upload/data_expression.txt" + + def __init__(self, parent): + super().__init__(parent) + name_pattern = self.config["expression_tool"] + ".{library_name}" + self.input_tpl = os.path.join( + self.config["path_ngs_mapping"], + "output", + name_pattern, + "out", + name_pattern + ".GeneCounts.tab", + ) + + def get_args(self, action): # Validate action self._validate_action(action) - yield from self.iterate_over_biomedsheets(action) + return { + "action_type": "expression", + "extra_args": { + "pipeline_id": "ENSEMBL", + "tx_obj": self.parent.w_config["step_config"]["ngs_mapping"][ + self.config["expression_tool"] + ]["path_features"], + }, + } def get_resource_usage(self, action): """Get Resource Usage @@ -352,37 +558,147 @@ def get_resource_usage(self, action): self._validate_action(action) return ResourceUsage( threads=2, - time="01:00:00", # 1 hour - memory="8G", + time="02:00:00", # 2 hours + memory="8192M", ) -class cbioportalZscoresStepPart(cbioportalExportStepPart): - """Generate a dataframe holding each biosample and the location of the CNV - calling results and the expression quantification files""" +class cbioportalMetaFilesStepPart(BaseStepPart): + """Generate cbioportal meta data files""" #: Step name - name = "cbioportal_zscores" + name = "cbioportal_meta_files" - def get_input_files(self, action): - assert action == "get_zscores_input" - yield from self.iterate_over_biomedsheets(action) - - def get_df(self, output): - with open(output[0], "w") as f: - writer = csv.writer(f, delimiter="\t") - writer.writerow(["ID", "gene_call_filename", "count_filename"]) - for sample_name, cnv_file, exp_file in self.iterate_over_biomedsheets( - "get_zscores_input" + #: Actions + actions = ("run",) + + def get_output_files(self, action): + # Validate action + self._validate_action(action) + yield from [os.path.join("work/upload", f) for f in META_FILES["always_present"]] + if self.config["path_somatic_variant"]: + yield from [os.path.join("work/upload", f) for f in META_FILES["sequenced"]] + if self.config["path_copy_number"]: + yield from [os.path.join("work/upload", f) for f in META_FILES["cna"]] + if self.config["study"]["reference_genome"] == "hg19": + yield from [os.path.join("work/upload", f) for f in META_FILES["segment"]] + if self.config["path_ngs_mapping"]: + yield from [os.path.join("work/upload", f) for f in META_FILES["rna_seq_mrna"]] + + +class cbioportalClinicalDataStepPart(cbioportalExportStepPart): + """Generate cbioportal patient data file""" + + #: Step name + name = "cbioportal_clinical_data" + + #: Actions + actions = ("run",) + + def get_args(self, action): + # Validate action + self._validate_action(action) + donors = {} + for extraction_type in ("DNA", "RNA"): + if ( + extraction_type == "DNA" + and self.config["path_somatic_variant"] == "" + and self.config["path_copy_number"] == "" ): - writer.writerow([sample_name, cnv_file, exp_file]) + continue + if extraction_type == "RNA" and self.config["path_ngs_mapping"] == "": + continue + self.extraction_type = extraction_type + for lib in self._yield_libraries(): + assert lib.test_sample.extra_infos["extractionType"] == extraction_type + donor_name = lib.test_sample.bio_sample.bio_entity.name + sample_name = lib.test_sample.bio_sample.name + if donor_name not in donors: + donors[donor_name] = {} + if sample_name not in donors[donor_name]: + donors[donor_name][sample_name] = {} + # Multiple libraries should not be returned by _yield_libraries + assert extraction_type not in donors[donor_name][sample_name] + donors[donor_name][sample_name][extraction_type] = lib.name + return donors + @dictify + def get_output_files(self, action): + # Validate action + self._validate_action(action) + for data_type in ("patient", "sample"): + yield data_type, "work/upload/data_clinical_{data_type}.txt".format(data_type=data_type) -class CbioportalComputeZscoresStepPart(cbioportalExportStepPart): - """Compute Z-Scores""" + +class cbioportalCaseListsStepPart(cbioportalExportStepPart): + """Generate cbioportal patient data file""" #: Step name - name = "cbioportal_compute_zscores" + name = "cbioportal_case_lists" + + #: Actions + actions = ("run",) + + def get_args(self, action): + # Validate action + self._validate_action(action) + samples = dict(zip(CASE_LIST_FILES.keys(), [[] for _ in range(len(CASE_LIST_FILES))])) + self.extraction_type = "DNA" + for lib in self._yield_libraries(): + sample_name = lib.test_sample.bio_sample.name + if self.config["path_somatic_variant"]: + samples["sequenced"] += [sample_name] + if self.config["path_copy_number"]: + samples["cna"] += [sample_name] + if self.config["path_somatic_variant"] and self.config["path_copy_number"]: + samples["cnaseq"] += [sample_name] + if self.config["path_ngs_mapping"]: + self.extraction_type = "RNA" + for lib in self._yield_libraries(): + sample_name = lib.test_sample.bio_sample.name + samples["rna_seq_mrna"] += [sample_name] + args = {} + for k, v in samples.items(): + if len(v) > 0: + args[k] = CASE_LIST_FILES[k] + args[k]["samples"] = v + if ( + self.config["path_somatic_variant"] + and self.config["path_copy_number"] + and self.config["path_ngs_mapping"] + ): + args["3way_complete"] = CASE_LIST_FILES["3way_complete"] + args["3way_complete"]["samples"] = [] + for sample_name in args["cnaseq"]["samples"]: + if sample_name in args["rna_seq_mrna"]["samples"]: + args["3way_complete"]["samples"] += [sample_name] + return args + + @dictify + def get_output_files(self, action): + # Validate action + self._validate_action(action) + case_lists = {} + if self.config["path_somatic_variant"]: + case_lists["sequenced"] = CASE_LIST_FILES["sequenced"]["filename"] + if self.config["path_copy_number"]: + case_lists["cna"] = CASE_LIST_FILES["cna"]["filename"] + if self.config["path_ngs_mapping"]: + case_lists["rna_seq_mrna"] = CASE_LIST_FILES["rna_seq_mrna"]["filename"] + if self.config["path_somatic_variant"]: + if self.config["path_copy_number"]: + case_lists["cnaseq"] = CASE_LIST_FILES["cnaseq"]["filename"] + if self.config["path_ngs_mapping"]: + case_lists["3way_complete"] = CASE_LIST_FILES["3way_complete"]["filename"] + for case, filename in case_lists.items(): + yield case, os.path.join("work/upload/case_lists", filename) + + +# ================================================================================================ +# +# cBioPortal step class +# +# ================================================================================================ class cbioportalExportWorkflow(BaseStep): @@ -410,69 +726,109 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) config_lookup_paths, config_paths, workdir, - (NgsMappingWorkflow,), ) + + # cBioPortal requires the genome release as GRC[hm]3[78] in the MAF file + # and hg19 or hg38 in the meta study & meta segment files. + # Note that segmentation visualisation is not yet implemented for hg38 (2023-06-21) + # For the user's convenience, the configuration is augmented automatically, + # before the sub steps are registered, so they all have the updated config. + translated = "unknown" + if self.config["vcf2maf"]["ncbi_build"] == "GRCh37": + translated = "hg19" + if self.config["vcf2maf"]["ncbi_build"] == "GRCh38": + translated = "hg38" + if self.config["vcf2maf"]["ncbi_build"] in ("mm9", "mm10", "GRCm37", "GRCm38", "GRCm39"): + translated = "mouse" + self.config["study"]["reference_genome"] = translated + # Register sub step classes so the sub steps are available self.register_sub_step_classes( ( - CbioportalStudyMetaFilesStepPart, cbioportalMetaFilesStepPart, cbioportalCaseListsStepPart, cbioportalClinicalDataStepPart, + cbioportalCns2CnaStepPart, cbioportalCnaFilesStepPart, - cbioportalMafStepPart, + cbioportalSegmentStepPart, + cbioportalMutationsStepPart, cbioportalVcf2MafStepPart, - cbioportalZscoresStepPart, - CbioportalComputeZscoresStepPart, - LinkOutStepPart, + cbioportalExpressionStepPart, ) ) # Initialize sub-workflows - if self.config["path_somatic_variant_filtration"]: - self.register_sub_workflow( - "somatic_variant_filtration", self.config["path_somatic_variant_filtration"] - ) - if self.config["path_gene_expression_quantification"]: - self.register_sub_workflow( - "gene_expression_quantification", self.config["path_gene_expression_quantification"] - ) - if self.config["path_copy_number_step"]: - if self.config["cnv_tool"] in ["cnvetti_on_target_postprocess", "copywriter"]: + if self.config["path_somatic_variant"]: + if self.config["filter_set"]: + self.register_sub_workflow( + "somatic_variant_filtration", + self.config["path_somatic_variant"], + sub_workflow_name="somatic_variant", + ) + else: + self.register_sub_workflow( + "somatic_variant_annotation", + self.config["path_somatic_variant"], + sub_workflow_name="somatic_variant", + ) + if self.config["path_copy_number"]: + if self.config["copy_number_tool"] in [ + "cnvetti_on_target_postprocess", + "copywriter", + "cnvkit", + ]: self.register_sub_workflow( "somatic_targeted_seq_cnv_calling", - workdir=self.config["path_copy_number_step"], + workdir=self.config["path_copy_number"], sub_workflow_name="copy_number_step", ) else: self.register_sub_workflow( "somatic_wgs_cnv_calling", - workdir=self.config["path_copy_number_step"], + workdir=self.config["path_copy_number"], sub_workflow_name="copy_number_step", ) - - if not self.config.get("tools_somatic_variant_calling", ""): - self.config["tools_somatic_variant_calling"] = self.w_config["step_config"][ - "somatic_variant_calling" - ]["tools"] + if self.config["path_ngs_mapping"]: + self.register_sub_workflow( + "ngs_mapping", + workdir=self.config["path_ngs_mapping"], + sub_workflow_name="ngs_mapping", + ) @listify def get_result_files(self): - result_files = ("meta_study.txt",) + META_FILES + CLINICAL_DATA_FILES - if self.config["path_somatic_variant_filtration"]: - result_files += ("data_mutation_extended.txt",) - result_files += ("case_lists/all_cases_with_mutation_data.txt",) - if self.config["path_copy_number_step"]: - result_files += CNA_DATA_FILES - if self.config["path_gene_expression_quantification"]: - result_files += ("data_expression_zscores.txt",) - - yield from [os.path.join("work/upload", f) for f in result_files] + yield from self.sub_steps["cbioportal_meta_files"].get_output_files("run") + yield from self.sub_steps["cbioportal_clinical_data"].get_output_files("run").values() + yield from self.sub_steps["cbioportal_case_lists"].get_output_files("run").values() + + result_files = [] + if self.config["path_somatic_variant"]: + result_files += [self.sub_steps["cbioportal_mutations"].get_output_files("run")] + if self.config["path_copy_number"]: + result_files += [self.sub_steps["cbioportal_cna"].get_output_files("log2")] + result_files += [self.sub_steps["cbioportal_cna"].get_output_files("gistic")] + if self.config["study"]["reference_genome"] == "hg19": + result_files += [self.sub_steps["cbioportal_segment"].get_output_files("run")] + if self.config["path_ngs_mapping"]: + result_files += [self.sub_steps["cbioportal_expression"].get_output_files("run")] + + yield from result_files def check_config(self): """Check config attributes for presence""" - if self.config["cnv_tool"] not in [ - "cnvetti_on_target_postprocess", - "copywriter", - "control_freec", - ]: - raise MissingConfiguration(msg="Please select a supported tool for the CNV calls") + msg = [] + if self.config["path_somatic_variant"] and ( + not self.config["somatic_variant_calling_tool"] + or not self.config["somatic_variant_annotation_tool"] + ): + msg += [ + "Somatic variant calling tool and somatic variant annotation tool must be defined" + ] + if self.config["path_copy_number"] and not self.config["copy_number_tool"]: + msg += [ + "Somatic copy number calling tool must be defined when CNV results are available" + ] + if self.config["path_ngs_mapping"] and not self.config["expression_tool"]: + msg += ["Gene count tools must be defined when RNA expression is available"] + if len(msg) > 0: + raise MissingConfiguration() # (msg="Please select a supported tool for the CNV calls") + return 0 diff --git a/snappy_pipeline/workflows/ngs_mapping/Snakefile b/snappy_pipeline/workflows/ngs_mapping/Snakefile index edf6252b2..8e9bedb9e 100644 --- a/snappy_pipeline/workflows/ngs_mapping/Snakefile +++ b/snappy_pipeline/workflows/ngs_mapping/Snakefile @@ -242,3 +242,50 @@ rule ngs_mapping_ngs_chew_fingerprint: **wf.get_log_file("ngs_chew", "fingerprint"), wrapper: wf.wrapper_path("ngs_chew/fingerprint") + + +# Compute protocol strandedness for STAR -------------------------------------- + + +rule ngs_mapping_infer_strandedness: + input: + **wf.get_input_files("strandedness", "infer"), + output: + **wf.get_output_files("strandedness", "infer"), + threads: wf.get_resource("strandedness", "infer", "threads") + resources: + time=wf.get_resource("strandedness", "infer", "time"), + memory=wf.get_resource("strandedness", "infer", "memory"), + partition=wf.get_resource("strandedness", "infer", "partition"), + tmpdir=wf.get_resource("strandedness", "infer", "tmpdir"), + log: + **wf.get_log_file("strandedness", "infer"), + wrapper: + wf.wrapper_path("rseqc") + + +# Gene counts from mapper & strandedness -------------------------------------- + + +rule ngs_mapping_counts_with_strand: + input: + **wf.get_input_files("strandedness", "counts"), + output: + **wf.get_output_files("strandedness", "counts"), + shell: + r""" + set -x + if [[ "{wildcards[mapper]}" == "star" ]] + then + strand=$(grep -E '^ *"decision": "[012]"$' {input.decision} | sed -re 's/.*"([012])"$/\1/') + column=$(($strand + 2)) + cut -f 1,$column {input.counts} > {output.counts} + else + ln -sr {input.counts} {output.counts} + fi + pushd $(dirname {output.counts}) + md5sum $(basename {output.counts}) > $(basename {output.counts_md5}) + popd + ln -sr {output.counts} {output.output} + ln -sr {output.counts_md5} {output.output_md5} + """ diff --git a/snappy_pipeline/workflows/ngs_mapping/__init__.py b/snappy_pipeline/workflows/ngs_mapping/__init__.py index 41076f46e..6e40acacb 100644 --- a/snappy_pipeline/workflows/ngs_mapping/__init__.py +++ b/snappy_pipeline/workflows/ngs_mapping/__init__.py @@ -410,6 +410,10 @@ trim_adapters: false mask_duplicates: false include_unmapped: true + strandedness: + path_exon_bed: REQUIRED # Location of usually highly expressed genes. Known protein coding genes is a good choice + strand: -1 # -1: unknown value, use infer_, 0: unstranded, 1: forward, 2: reverse (from featurecounts) + threshold: 0.85 # Minimum proportion of reads mapped to forward/reverse direction to call the protocol # Configuration for Minimap2 minimap2: mapping_threads: 16 @@ -809,6 +813,23 @@ def _get_output_files_run_work(self): output_files["transcriptome_md5"] = output_files["transcriptome"] + ".md5" return output_files + @dictify + def get_output_files(self, action): + """Skip link to the gene counts file to delegate it to strandedness""" + assert action in self.actions + for key, paths in super().get_output_files(action).items(): + if key != "output_links": + yield key, paths + continue + yield key, list( + filter( + lambda x: not ( + x.endswith(".GeneCounts.tab") or x.endswith(".GeneCounts.tab.md5") + ), + paths, + ) + ) + def get_resource_usage(self, action): """Get Resource Usage @@ -831,6 +852,91 @@ def get_resource_usage(self, action): ) +class StrandednessStepPart(BaseStepPart): + """Guess the protocol strandedness when missing and write it""" + + #: Step name + name = "strandedness" + + #: Class available actions + actions = ("infer", "counts") + + def get_input_files(self, action): + self._validate_action(action) + if action == "infer": + return { + "bam": "work/{mapper}.{library_name}/out/{mapper}.{library_name}.bam", + } + elif action == "counts": + return { + "counts": "work/{mapper}.{library_name}/out/{mapper}.{library_name}.GeneCounts.tab", + "decision": "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.decision.json", + } + + @dictify + def get_output_files(self, action): + self._validate_action(action) + if action == "infer": + for key, ext in (("tsv", ".infer.txt"), ("decision", ".decision.json")): + yield key, "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}" + ext + yield key + "_md5", "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}" + ext + ".md5" + key, ext = ("output", ".decision.json") + yield key, "output/{mapper}.{library_name}/strandedness/{mapper}.{library_name}" + ext + yield key + "_md5", "output/{mapper}.{library_name}/strandedness/{mapper}.{library_name}" + ext + ".md5" + for key, ext in ( + ("log", ".log"), + ("conda_list", ".conda_list.txt"), + ("conda_info", ".conda_info.txt"), + ): + yield key, "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness" + ext + yield key + "_md5", "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness" + ext + ".md5" + elif action == "counts": + key, ext = ("counts", ".GeneCounts.tab") + yield key, "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}" + ext + yield key + "_md5", "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}" + ext + ".md5" + key, ext = ("output", ".GeneCounts.tab") + yield key, "output/{mapper}.{library_name}/out/{mapper}.{library_name}" + ext + yield key + "_md5", "output/{mapper}.{library_name}/out/{mapper}.{library_name}" + ext + ".md5" + + def get_result_files(self): + for mapper in self.config["tools"]["rna"]: + if self.config[mapper]["path_features"]: + tpl_out = ( + "output/{mapper}.{library_name}/out/{mapper}.{library_name}.GeneCounts.tab" + ) + tpl_strandedness = "output/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.decision.json" + tpl_log = ( + "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.{ext}" + ) + for library_name, extra_info in self.parent.ngs_library_to_extra_infos.items(): + if extra_info["extractionType"] == "RNA": + yield tpl_out.format(mapper=mapper, library_name=library_name) + yield tpl_out.format(mapper=mapper, library_name=library_name) + ".md5" + yield tpl_strandedness.format(mapper=mapper, library_name=library_name) + yield tpl_strandedness.format( + mapper=mapper, library_name=library_name + ) + ".md5" + for ext in ("log", "conda_info.txt", "conda_list.txt"): + yield tpl_log.format(mapper=mapper, library_name=library_name, ext=ext) + yield tpl_log.format( + mapper=mapper, library_name=library_name, ext=ext + ) + ".md5" + + @dictify + def get_log_file(self, action): + """Return dict of log files in the "log" directory.""" + _ = action + prefix = "work/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness" + key_ext = ( + ("log", ".log"), + ("conda_info", ".conda_info.txt"), + ("conda_list", ".conda_list.txt"), + ) + for key, ext in key_ext: + yield key, prefix + ext + yield key + "_md5", prefix + ext + ".md5" + + class Minimap2StepPart(ReadMappingStepPart): """Support for performing long-read alignment using minimap2""" @@ -1260,6 +1366,7 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) LinkInStep, Minimap2StepPart, StarStepPart, + StrandednessStepPart, TargetCoverageReportStepPart, BamCollectDocStepPart, NgsChewStepPart, diff --git a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py index 4e017c21f..ddea1c5f7 100644 --- a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py +++ b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py @@ -101,7 +101,7 @@ import os.path import sys -from biomedsheets.shortcuts import CancerCaseSheet, is_not_background +from biomedsheets.shortcuts import CancerCaseSheet, CancerCaseSheetOptions, is_not_background from snakemake.io import expand from snappy_pipeline.utils import dictify, listify @@ -126,6 +126,7 @@ path_target: REQUIRED # Usually ../panel_of_normals/output/cnvkit.target/out/cnvkit.target.bed path_antitarget: REQUIRED # Usually ../panel_of_normals/output/cnvkit.antitarget/out/cnvkit.antitarget.bed path_panel_of_normals: REQUIRED # Usually ../panel_of_normals/output/{mapper}.cnvkit.create_panel/out/{mapper}.cnvkit.panel_of_normals.cnn + plot: True # Generate plots (very slow) min_mapq: 0 # [coverage] Mininum mapping quality score to count a read for coverage depth count: False # [coverage] Alternative couting algorithm gc_correction: True # [fix] Use GC correction @@ -431,6 +432,7 @@ class CnvKitStepPart(SomaticTargetedSeqCnvCallingStepPart): "fix", "segment", "call", + "postprocess", "export", "plot", "report", @@ -484,6 +486,7 @@ def get_input_files(self, action): "call": self._get_input_files_call, "fix": self._get_input_files_fix, "segment": self._get_input_files_segment, + "postprocess": self._get_input_files_postprocess, "export": self._get_input_files_export, "plot": self._get_input_files_plot, "report": self._get_input_files_report, @@ -524,9 +527,25 @@ def _get_input_files_call(wildcards): input_files = {"segment": segment_pattern.format(**wildcards)} return input_files + @staticmethod + def _get_input_files_postprocess(wildcards): + segment_pattern = ( + "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.segment.cns" + ) + call_pattern = ( + "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.call.cns" + ) + input_files = { + "segment": segment_pattern.format(**wildcards), + "call": call_pattern.format(**wildcards), + } + return input_files + @staticmethod def _get_input_files_export(wildcards): - cns_pattern = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.cns" + cns_pattern = ( + "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.call.cns" + ) input_files = {"cns": cns_pattern.format(**wildcards)} return input_files @@ -535,7 +554,7 @@ def _get_input_files_plot(wildcards): tpl = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.{ext}" input_files = { "cnr": tpl.format(ext="cnr", **wildcards), - "cns": tpl.format(ext="cns", **wildcards), + "cns": tpl.format(ext="call.cns", **wildcards), } return input_files @@ -545,7 +564,7 @@ def _get_input_files_report(self, wildcards): "target": tpl.format(ext="targetcoverage.cnn", **wildcards), "antitarget": tpl.format(ext="antitargetcoverage.cnn", **wildcards), "cnr": tpl.format(ext="cnr", **wildcards), - "cns": tpl.format(ext="cns", **wildcards), + "cns": tpl.format(ext="call.cns", **wildcards), } return input_files @@ -559,6 +578,8 @@ def get_output_files(self, action): return self._get_output_files_segment() elif action == "call": return self._get_output_files_call() + elif action == "postprocess": + return self._get_output_files_postprocess() elif action == "export": return self._get_output_files_export() elif action == "plot": @@ -594,9 +615,15 @@ def _get_output_files_segment(): @staticmethod def _get_output_files_call(): name_pattern = "{mapper}.cnvkit.{library_name}" - tpl = os.path.join("work", name_pattern, "out", name_pattern + ".cns") + tpl = os.path.join("work", name_pattern, "out", name_pattern + ".call.cns") return {"calls": tpl, "calls_md5": tpl + ".md5"} + @staticmethod + def _get_output_files_postprocess(): + name_pattern = "{mapper}.cnvkit.{library_name}" + tpl = os.path.join("work", name_pattern, "out", name_pattern + ".cns") + return {"final": tpl, "final_md5": tpl + ".md5"} + @dictify def _get_output_files_plot(self): plots = (("diagram", "pdf"), ("heatmap", "pdf"), ("scatter", "png")) @@ -858,6 +885,10 @@ class SomaticTargetedSeqCnvCallingWorkflow(BaseStep): #: Default biomed sheet class sheet_shortcut_class = CancerCaseSheet + sheet_shortcut_kwargs = { + "options": CancerCaseSheetOptions(allow_missing_normal=True, allow_missing_tumor=True) + } + @classmethod def default_config_yaml(cls): """Return default config YAML, to be overwritten by project-specific one""" @@ -889,11 +920,13 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) def get_result_files(self): """Return list of result files for the somatic targeted sequencing CNV calling step""" tool_actions = { - "cnvkit": ("fix", "call", "report", "export", "plot"), + "cnvkit": ["fix", "postprocess", "report", "export"], "copywriter": ("call",), "cnvetti_on_target": ("coverage", "segment", "postprocess"), "cnvetti_off_target": ("coverage", "segment", "postprocess"), } + if "cnvkit" in self.config["tools"] and self.config["cnvkit"]["plot"]: + tool_actions["cnvkit"] += ["plot"] for sheet in filter(is_not_background, self.shortcut_sheets): for sample_pair in sheet.all_sample_pairs: if ( diff --git a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/cnvkit.rules b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/cnvkit.rules index 4014660c1..1281eff3d 100644 --- a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/cnvkit.rules +++ b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/cnvkit.rules @@ -66,6 +66,23 @@ rule somatic_targeted_seq_cnv_calling_cnvkit_call: wf.wrapper_path("cnvkit/call") +rule somatic_targeted_seq_cnv_calling_cnvkit_postprocess: + input: + unpack(wf.get_input_files("cnvkit", "postprocess")), + output: + **wf.get_output_files("cnvkit", "postprocess"), + threads: wf.get_resource("cnvkit", "postprocess", "threads") + resources: + time=wf.get_resource("cnvkit", "postprocess", "time"), + memory=wf.get_resource("cnvkit", "postprocess", "memory"), + partition=wf.get_resource("cnvkit", "postprocess", "partition"), + tmpdir=wf.get_resource("cnvkit", "postprocess", "tmpdir"), + log: + **wf.get_log_file("cnvkit", "postprocess"), + wrapper: + wf.wrapper_path("cnvkit/postprocess") + + rule somatic_targeted_seq_cnv_calling_cnvkit_plot: input: unpack(wf.get_input_files("cnvkit", "plot")), diff --git a/snappy_pipeline/workflows/somatic_wgs_cnv_calling/__init__.py b/snappy_pipeline/workflows/somatic_wgs_cnv_calling/__init__.py index 6cbfdf4e2..2785acb1d 100644 --- a/snappy_pipeline/workflows/somatic_wgs_cnv_calling/__init__.py +++ b/snappy_pipeline/workflows/somatic_wgs_cnv_calling/__init__.py @@ -140,6 +140,7 @@ path_target: REQUIRED # Usually ../panel_of_normals/output/cnvkit.target/out/cnvkit.target.bed path_antitarget: REQUIRED # Usually ../panel_of_normals/output/cnvkit.antitarget/out/cnvkit.antitarget.bed path_panel_of_normals: REQUIRED # Usually ../panel_of_normals/output/{mapper}.cnvkit.create_panel/out/{mapper}.cnvkit.panel_of_normals.cnn + plot: True # Output plots (very slow) min_mapq: 0 # [coverage] Mininum mapping quality score to count a read for coverage depth count: False # [coverage] Alternative couting algorithm gc_correction: True # [fix] Use GC correction @@ -448,6 +449,7 @@ class CnvkitSomaticWgsStepPart(SomaticWgsCnvCallingStepPart): "fix", "segment", "call", + "postprocess", "export", "plot", "report", @@ -501,6 +503,7 @@ def get_input_files(self, action): "call": self._get_input_files_call, "fix": self._get_input_files_fix, "segment": self._get_input_files_segment, + "postprocess": self._get_input_files_postprocess, "export": self._get_input_files_export, "plot": self._get_input_files_plot, "report": self._get_input_files_report, @@ -541,9 +544,19 @@ def _get_input_files_call(wildcards): input_files = {"segment": segment_pattern.format(**wildcards)} return input_files + @staticmethod + def _get_input_files_postprocess(wildcards): + segment_pattern = ( + "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.call.cns" + ) + input_files = {"call": segment_pattern.format(**wildcards)} + return input_files + @staticmethod def _get_input_files_export(wildcards): - cns_pattern = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.cns" + cns_pattern = ( + "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.call.cns" + ) input_files = {"cns": cns_pattern.format(**wildcards)} return input_files @@ -552,7 +565,7 @@ def _get_input_files_plot(wildcards): tpl = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.{ext}" input_files = { "cnr": tpl.format(ext="cnr", **wildcards), - "cns": tpl.format(ext="cns", **wildcards), + "cns": tpl.format(ext="call.cns", **wildcards), } return input_files @@ -562,7 +575,7 @@ def _get_input_files_report(self, wildcards): "target": tpl.format(ext="targetcoverage.cnn", **wildcards), "antitarget": tpl.format(ext="antitargetcoverage.cnn", **wildcards), "cnr": tpl.format(ext="cnr", **wildcards), - "cns": tpl.format(ext="cns", **wildcards), + "cns": tpl.format(ext="call.cns", **wildcards), } return input_files @@ -574,6 +587,7 @@ def get_output_files(self, action): "coverage": self._get_output_files_coverage, "fix": self._get_output_files_fix, "call": self._get_output_files_call, + "postprocess": self._get_output_files_postprocess, "segment": self._get_output_files_segment, "export": self._get_output_files_export, "plot": self._get_output_files_plot, @@ -607,9 +621,15 @@ def _get_output_files_segment(): @staticmethod def _get_output_files_call(): name_pattern = "{mapper}.cnvkit.{library_name}" - tpl = os.path.join("work", name_pattern, "out", name_pattern + ".cns") + tpl = os.path.join("work", name_pattern, "out", name_pattern + ".call.cns") return {"calls": tpl, "calls_md5": tpl + ".md5"} + @staticmethod + def _get_output_files_postprocess(): + name_pattern = "{mapper}.cnvkit.{library_name}" + tpl = os.path.join("work", name_pattern, "out", name_pattern + ".cns") + return {"final": tpl, "final_md5": tpl + ".md5"} + @dictify def _get_output_files_plot(self): plots = (("diagram", "pdf"), ("heatmap", "pdf"), ("scatter", "png")) @@ -909,16 +929,21 @@ def get_result_files(self): mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], caller="cnvkit", ) - plots = (("diagram", "pdf", False), ("heatmap", "pdf", True), ("scatter", "png", True)) - yield from self._yield_report_files( - ( - "output/{mapper}.{caller}.{cancer_library.name}/report/" - "{mapper}.{caller}.{cancer_library.name}.{ext}" - ), - plots, - mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], - caller="cnvkit", - ) + if self.config["cnvkit"]["plot"]: + plots = ( + ("diagram", "pdf", False), + ("heatmap", "pdf", True), + ("scatter", "png", True), + ) + yield from self._yield_report_files( + ( + "output/{mapper}.{caller}.{cancer_library.name}/report/" + "{mapper}.{caller}.{cancer_library.name}.{ext}" + ), + plots, + mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], + caller="cnvkit", + ) if "cnvetti" in bcf_tools: for sheet in filter(is_not_background, self.shortcut_sheets): for donor in sheet.donors: diff --git a/snappy_pipeline/workflows/somatic_wgs_cnv_calling/cnvkit.rules b/snappy_pipeline/workflows/somatic_wgs_cnv_calling/cnvkit.rules index 5e91bd261..b6cd0c49f 100644 --- a/snappy_pipeline/workflows/somatic_wgs_cnv_calling/cnvkit.rules +++ b/snappy_pipeline/workflows/somatic_wgs_cnv_calling/cnvkit.rules @@ -62,6 +62,22 @@ rule somatic_wgs_cnv_calling_cnvkit_call: wf.wrapper_path("cnvkit/call") +rule somatic_wgs_cnv_calling_cnvkit_postprocess: + input: + unpack(wf.get_input_files("cnvkit", "postprocess")), + output: + **wf.get_output_files("cnvkit", "postprocess"), + threads: wf.get_resource("cnvkit", "postprocess", "threads") + resources: + time=wf.get_resource("cnvkit", "postprocess", "time"), + memory=wf.get_resource("cnvkit", "postprocess", "memory"), + partition=wf.get_resource("cnvkit", "postprocess", "partition"), + log: + **wf.get_log_file("cnvkit", "postprocess"), + wrapper: + wf.wrapper_path("cnvkit/postprocess") + + rule somatic_wgs_cnv_calling_cnvkit_plot: input: unpack(wf.get_input_files("cnvkit", "plot")), diff --git a/snappy_wrappers/wrappers/cbioportal/case_lists/wrapper.py b/snappy_wrappers/wrappers/cbioportal/case_lists/wrapper.py index 39ab48682..0b29e3302 100644 --- a/snappy_wrappers/wrappers/cbioportal/case_lists/wrapper.py +++ b/snappy_wrappers/wrappers/cbioportal/case_lists/wrapper.py @@ -3,32 +3,36 @@ input. Takes a dict from biomedsheets/snappy_pipeline, writes out all_cases_with_mutation_data.txt """ +import os -def write_case_list_sequenced(sheets, config, outfile): - """Takes a biomedsheet and writes a case list for all samples with DNA sequencing data""" - samples = [] - for sheet in sheets: - for p in sheet.bio_entities.values(): - for s in p.bio_samples.values(): - if s.extra_infos["isTumor"]: - samples.append(s.name) - samples = list(set(samples)) +def write_case_list(args, outfile): + """Takes a biomedsheet and writes a case list for all samples with DNA sequencing data""" + category = os.path.basename(outfile).replace(".txt", "") with open(outfile, "w") as f: s = "\n".join( [ "cancer_study_identifier: {cancer_study_id}", - "stable_id: {cancer_study_id}_sequenced", - "case_list_name: Sequenced tumors", - "case_list_description: Sequenced tumor samples", - "case_list_category: all_cases_with_mutation_data", + "stable_id: {cancer_study_id}_{stable_id}", + "case_list_name: {name}", + "case_list_description: {description}", + "case_list_category: {category}", "case_list_ids: {all_samples}", + "", ] ).format( - cancer_study_id=config["step_config"]["cbioportal_export"]["cancer_study_id"], - all_samples="\t".join(samples), + cancer_study_id=snakemake.config["step_config"]["cbioportal_export"]["study"][ + "cancer_study_id" + ], + stable_id=args["stable_id"], + name=args["name"], + description=args["description"], + category=args["category"], + all_samples="\t".join(args["samples"]), ) f.write(s) -write_case_list_sequenced(snakemake.params.sheet, snakemake.config, snakemake.output.sequenced) +for case_list, filename in snakemake.output.items(): + assert case_list in snakemake.params.keys() + write_case_list(snakemake.params[case_list], filename) diff --git a/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py b/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py index 511648816..65aae5b9a 100644 --- a/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py +++ b/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py @@ -5,9 +5,11 @@ import csv +import json +import os -def write_clinical_patient_tsv(sheets): +def write_clinical_patient_tsv(donors): """Takes a biomedsheet and writes a clinical patient tsv for cbioportal, see https://github.com/cBioPortal/cbioportal/blob/master/docs/File-Formats.md#the-patient-file for specification @@ -25,11 +27,7 @@ def write_clinical_patient_tsv(sheets): # attribute columns COLUMNS = ["PATIENT_ID", "DUMMY"] - patients = [] - for sheet in sheets: - patients += [bio_entity.name for bio_entity in sheet.bio_entities.values()] - - with open(snakemake.output.patients_tsv, "w") as tsvfile: + with open(snakemake.output.patient, "w") as tsvfile: writer = csv.writer(tsvfile, delimiter="\t") # write header writer.writerow(NAMES) @@ -38,16 +36,64 @@ def write_clinical_patient_tsv(sheets): writer.writerow(PRIORITY) writer.writerow(COLUMNS) - for p in patients: - writer.writerow([p, "UNKNOWN"]) + for donor in donors.keys(): + writer.writerow([donor, "UNKNOWN"]) + + +class SampleInfoTMB: + step = "tumor_mutational_burden" + name = "TMB" + description = "Tumor mutational burden computed on CDS regions" + datatype = "NUMBER" + priority = "2" + column = "TMB" + + def __init__(self, config, **kwargs): + name_pattern = "bwa." + kwargs["somatic_variant_tool"] + ".tmb.{library}" + self.tpl = os.path.join( + config["path"], "output", name_pattern, "out", name_pattern + ".json" + ) + def get_data(self, lib_by_extraction): + if "DNA" in lib_by_extraction: + library = lib_by_extraction["DNA"] + path = self.tpl.format(library=library) + try: + with open(path, "r") as f: + result = json.load(f) + return result["TMB"] + except Exception as e: + print( + "WARNING- error {} occured when extraction TMB for library {}".format( + e, library + ) + ) + else: + print("WARNING- no DNA data") + return "" -def write_clinical_samples_tsv(sheets): + +def write_clinical_samples_tsv(donors): """Takes a biomedsheet and writes a clinical sample tsv for cbioportal, see https://github.com/cBioPortal/cbioportal/blob/master/docs/File-Formats.md#the-samples-file for specification """ + sample_info_getters = [] + for extra_info in snakemake.config["step_config"]["cbioportal_export"]["sample_info"]: + step = extra_info["step"] + if step == "tumor_mutational_burden": + sample_info_getters.append( + SampleInfoTMB( + extra_info, + somatic_variant_tool=snakemake.config["step_config"]["cbioportal_export"][ + "somatic_variant_calling_tool" + ], + ) + ) + else: + raise Exception("Unknown sample info request") + # Header lines, first item must start with # # attribute Display Names NAMES = ["#Patient Identifier", "Sample Identifier"] @@ -60,7 +106,14 @@ def write_clinical_samples_tsv(sheets): # attribute columns COLUMNS = ["PATIENT_ID", "SAMPLE_ID"] - with open(snakemake.output.samples_tsv, "w") as tsvfile: + for extra_info in sample_info_getters: + NAMES += [extra_info.name] + DESC += [extra_info.description] + DATATYPE += [extra_info.datatype] + PRIORITY += [extra_info.priority] + COLUMNS += [extra_info.column] + + with open(snakemake.output.sample, "w") as tsvfile: writer = csv.writer(tsvfile, delimiter="\t") # write header writer.writerow(NAMES) @@ -69,12 +122,13 @@ def write_clinical_samples_tsv(sheets): writer.writerow(PRIORITY) writer.writerow(COLUMNS) - for sheet in sheets: - for p in sheet.bio_entities.values(): - for s in p.bio_samples.values(): - if s.extra_infos["isTumor"]: - writer.writerow([p.name, s.name]) + for donor, v in donors.items(): + for sample, vv in v.items(): + row = [donor, sample] + for extra_info in sample_info_getters: + row.append(extra_info.get_data(vv)) + writer.writerow(row) -write_clinical_patient_tsv(snakemake.params.sheet) -write_clinical_samples_tsv(snakemake.params.sheet) +write_clinical_patient_tsv(snakemake.params) +write_clinical_samples_tsv(snakemake.params) diff --git a/snappy_wrappers/wrappers/cbioportal/compute_signatures/environment.yaml b/snappy_wrappers/wrappers/cbioportal/compute_signatures/environment.yaml deleted file mode 100644 index 5c44fa731..000000000 --- a/snappy_wrappers/wrappers/cbioportal/compute_signatures/environment.yaml +++ /dev/null @@ -1,9 +0,0 @@ -channels: -- bioconda -- conda-forge -- anaconda -dependencies: -- r -- r-dplyr -- bioconductor-gsva -- bioconductor-cqn diff --git a/snappy_wrappers/wrappers/cbioportal/compute_signatures/wrapper.py b/snappy_wrappers/wrappers/cbioportal/compute_signatures/wrapper.py deleted file mode 100644 index 4cb1c948f..000000000 --- a/snappy_wrappers/wrappers/cbioportal/compute_signatures/wrapper.py +++ /dev/null @@ -1,82 +0,0 @@ -# -*- coding: utf-8 -*- -"""Wrapper for computing expression signatures from counts""" - -import os.path - -from snakemake import shell - -# import pprint -# pprint.pprint(snakemake.output.pdf) - -if len(snakemake.output.pdf) == 1: - snakemake.output.pdf = snakemake.output.pdf[0] -else: - raise - -sample_tpl = os.path.basename(os.path.dirname(os.path.dirname(snakemake.output.pdf))) -sample_dir = os.path.dirname(os.path.dirname(snakemake.output.pdf)) - -__author__ = "Clemens Messerschmidt " - -shell.executable("/bin/bash") - -shell( - r""" -set -x - -export TMPDIR=$(mktemp -d) -trap "rm -rf $TMPDIR" EXIT - -# Also pipe stderr to log file -if [[ -n "{snakemake.log}" ]]; then - if [[ "$(set +e; tty; set -e)" != "" ]]; then - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - exec 2> >(tee -a "{snakemake.log}" >&2) - else - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - echo "No tty, logging disabled" >"{snakemake.log}" - fi -fi - -# ------------------------------------------------------------------------------------------------- -# Write helper script and call R -# -cat <<"EOF" > $TMPDIR/compute_signatures.R -library( magrittr ) -library( methods ) # https://github.com/tidyverse/broom/issues/67 - -gene_exp = read.delim("{snakemake.input.tsv}", stringsAsFactors=FALSE) - -sample = make.names("{sample_tpl}") -idx = which(sample == names(gene_exp)) - -m = as.matrix(gene_exp) -sig_list = expression.signatures::get_signature_list(id = "Gene_symbol") - -ssGSEA = GSVA::gsva(expr = m, - gset.idx.list = sig_list, - method = "gsva", no.bootstraps = 0, - #method = "ssgsea", ssgsea.norm=T, - rnaseq = T, - parallel.sz = 0, - min.sz = 5) - -sigs = ssGSEA$es.obs - -dir.create("{sample_dir}") -pdf("{snakemake.output.pdf}") - -for (i in 1:nrow(sigs)) {{ - signature = rownames(sigs)[i] - plot(density(sigs[i, ]), main=rownames(sigs)[i]) - abline( v= sigs[i, sample], col=2, lwd=3) -}} -dev.off() - -warnings() -sessionInfo() -EOF - -Rscript --vanilla $TMPDIR/compute_signatures.R -""" -) diff --git a/snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml b/snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml new file mode 100644 index 000000000..1f257fe3a --- /dev/null +++ b/snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml @@ -0,0 +1,14 @@ +name: merge_tables + +channels: +- conda-forge +- bioconda +- r + +dependencies: +- r-base +- r-tidyverse +- r-igraph +- bioconductor-genomicranges +- bioconductor-genomicfeatures +- bioconductor-deseq2 diff --git a/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R b/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R new file mode 100644 index 000000000..6438e6b83 --- /dev/null +++ b/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R @@ -0,0 +1,32 @@ +require(magrittr) + +#' Compute discrete copy number & log2 on genes +#' +#' @param fn names of the cns file +#' @param tx_obj Bioconductor feature description object or its name (human by default, either TxDb or EnsDb), or GTF/GFF features file +#' +#' @example +cns_to_cna <- function(fn, tx_obj=TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene, pipeline_id="ENSEMBL") { + if (missing(fn) || is.null(fn) || !is.character(fn) || length(fn)!=1 || is.na(fn) || fn=="") + stop("Missing or illegal cns filename") + + tx_obj <- get_tx_object(tx_obj) + genes <- GenomicFeatures::genes(tx_obj) + stopifnot("gene_id" %in% colnames(GenomicRanges::mcols(genes))) + + segments <- read.table(fn, sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE) + if ("chromosome" %in% colnames(segments)) colnames(segments)[colnames(segments)=="chromosome"] <- "chrom" + stopifnot(all(c("cn", "log2", "chrom", "start", "end") %in% colnames(segments))) + + seg <- GenomicRanges::makeGRangesFromDataFrame(segments, seqnames.field="chrom", start.field="start", end.field="end", strand="*", keep.extra.columns=FALSE) + + i <- GenomicRanges::findOverlaps(genes, seg) + i <- split(S4Vectors::subjectHits(i), S4Vectors::queryHits(i)) + i <- unlist(i[lengths(i) == 1]) + + tbl <- data.frame(FeatureID=as.character(genes$gene_id), cn=NA, log2=NA) + colnames(tbl)[1] <- pipeline_id + tbl[as.numeric(names(i)),c("cn", "log2")] <- segments[i,c("cn", "log2")] + + tbl +} diff --git a/snappy_wrappers/wrappers/cbioportal/generate_cna/wrapper.py b/snappy_wrappers/wrappers/cbioportal/generate_cna/wrapper.py new file mode 100644 index 000000000..a26b42146 --- /dev/null +++ b/snappy_wrappers/wrappers/cbioportal/generate_cna/wrapper.py @@ -0,0 +1,62 @@ +# -*- coding: utf-8 -*- +"""Wrapper for merging multiple tables in R on shared columns""" + +import os + +from snakemake import shell + +__author__ = "Eric Blanc " + +r_script = os.path.abspath(os.path.join(os.path.dirname(__file__), "script.R")) +helper_functions = os.path.join(os.path.dirname(r_script), "..", "helper_functions.R") + +shell( + r""" +set -x + +# Write files for reproducibility ----------------------------------------------------------------- + +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +pushd $(dirname {snakemake.log.conda_list}) ; md5sum $(basename {snakemake.log.conda_list}) > $(basename {snakemake.log.conda_list_md5}) ; popd +pushd $(dirname {snakemake.log.conda_info}) ; md5sum $(basename {snakemake.log.conda_info}) > $(basename {snakemake.log.conda_info_md5}) ; popd + +# Also pipe stderr to log file -------------------------------------------------------------------- + +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Create auto-cleaned temporary directory --------------------------------------------------------- + +export TMPDIR=$(mktemp -d) +trap "rm -rf $TMPDIR" EXIT + +# Run the R script -------------------------------------------------------------------------------- + +R --vanilla --slave << __EOF +source("{helper_functions}") +source("{r_script}") +write.table( + cns_to_cna("{snakemake.input}", "{snakemake.params[features]}", "{snakemake.params[pipeline_id]}"), + file="{snakemake.output}", sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE +) +__EOF + +pushd $(dirname {snakemake.output}) ; md5sum $(basename {snakemake.output}) > $(basename {snakemake.output}).md5 ; popd +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +sleep 1s # try to wait for log file flush +pushd $(dirname {snakemake.log.log}) ; md5sum $(basename {snakemake.log.log}) > $(basename {snakemake.log.log_md5}) ; popd +""" +) diff --git a/snappy_wrappers/wrappers/cbioportal/helper_functions.R b/snappy_wrappers/wrappers/cbioportal/helper_functions.R new file mode 100644 index 000000000..2858fdfb9 --- /dev/null +++ b/snappy_wrappers/wrappers/cbioportal/helper_functions.R @@ -0,0 +1,408 @@ +require(magrittr) + +#' Extracts the feature names & one column of values from tab-delimited sample files +#' and return a data.frame with the values for each sample in the columns, and +#' the feature names as row name. +#' +#' @param fns named list or named vector of sample filenames. The names are the sample IDs +#' @param featureCol the name of the column containing the feature names in the sample files +#' @param valueCol the name of the column containing the values to be extracted from each sample file. +#' +#' @example +read_sample_files <- function(fns, featureCol, valueCol, header=TRUE) { + if (missing(fns) || is.null(fns)) + stop("Missing list of files") + if (is.list(fns)) { + stopifnot(all(lengths(fns) == 1)) + fns <- unlist(fns) + } + if (!is.character(fns) || any(is.na(fns)) || any(fns=="")) + stop("Missing file name") + if (is.null(names(fns))) + stop("Missing sample names") + if (missing(featureCol) || is.null(featureCol) || !is.character(featureCol) || length(featureCol)!=1 || is.na(featureCol) || featureCol=="") + stop("Missing or illegal feature column name") + if (missing(valueCol) || is.null(valueCol) || !is.character(valueCol) || length(valueCol)!=1 || is.na(valueCol) || valueCol=="") + stop("Missing or illegal column name for data extraction") + + tbl <- NULL + for (i in names(fns)) { + tmp <- read.table(fns[i], sep="\t", header=header, stringsAsFactors=FALSE, check.names=FALSE) + stopifnot(all(c(featureCol, valueCol) %in% colnames(tmp))) + tmp <- tmp[,c(featureCol, valueCol),drop=FALSE] + colnames(tmp)[2] <- i + if (is.null(tbl)) { + tbl <- tmp + } else { + tbl <- tbl %>% dplyr::full_join(tmp, by=featureCol) + } + } + tbl <- tbl[!grepl("_PAR_Y$", tbl[[featureCol]]),,drop=FALSE] + if (any(duplicated(tbl[[featureCol]]))) + stop("Duplicated feature ids") + rownames(tbl) <- tbl[[featureCol]] + tbl[,colnames(tbl)!=featureCol,drop=FALSE] +} + + +#' Remap data to different feature ID (typically from ENSEMBL to SYMBOL or ENTREZ_ID). +#' +#' When the mappings between ids is not 1-1, the following rules are applied: +#' many-many relationships are removed +#' when pipeline id maps to multiple symbols, the data is copied to all symbols +#' when multiple pipeline ids map to a single symbol, the the method is taken into account: +#' when method is sum, the data for the target id is the sum of all "source" id for every sample, +#' when method is max, the data of the "source" id which is highest over all samples is selected as representative for the "target" id. +#' +#' @param mat the matrix or data.frame containing the data (expression, CNA, ...) +#' @param mappings the data frame of feature id mappings +#' @param from the "source" type of feature ids, must be in the mapping table column names +#' @param to the "target" type of feature ids, must be in the mapping table column names +#' @param method aggregation method when many "source" ids are mapped to the same "target" id +#' +#' @example +map_feature_id <- function(mat, mappings, from, to, method=c("sum", "max", "maxabs")) { + if (missing(mat) || is.null(mat) || !(is.data.frame(mat) || is.matrix(mat)) || nrow(mat)<1 || ncol(mat)<1) + stop("Missing or illegal data") + method <- match.arg(method) + if (missing(from) || is.null(from) || !is.character(from) || length(from)!=1 || is.na(from) || from=="") + stop("Missing or illegal feature id type (origin)") + if (missing(to) || is.null(to) || !is.character(to) || length(to)!=1 || is.na(to) || to=="") + stop("Missing or illegal feature id type (target)") + if (from==to) return(mat) + if (missing(mappings) || is.null(mappings) || !is.data.frame(mappings) || nrow(mappings)<1 || ncol(mappings)<2) + stop("Missing or illegal feature id mapping table") + if (!all(c(from, to) %in% colnames(mappings))) + stop("Feature id type ", from, " or ", to, " not in mappings table") + + mappings <- mappings[,c(from, to)] %>% dplyr::distinct() + mappings <- mappings[mappings[[from]] %in% rownames(mat),,drop=FALSE] + + n <- sum(rownames(mat) %in% mappings[[from]]) + if (n == 0) + stop("No common feature id between the mapping table and the data") + if (n/nrow(mat) < 0.9) + warning("The proportion of feature id that can be mapped is low at ", n/nrow(mat)) + if (n < nrow(mat)) + warning(nrow(mat) - n, " features cannot be mapped, removed from data") + mat <- mat[rownames(mat) %in% mappings[[from]],,drop=FALSE] + mappings <- mappings[mappings[[from]] %in% rownames(mat),,drop=FALSE] + + # Resolve 1-1, 1-many & many-1 mappings between ENSEMBL & HGNC symbols + mappings <- map_between_two_ids(mappings[[from]], mappings[[to]], haveIndex=FALSE, verbose=TRUE, keepBlanks=FALSE) + rslt <- NULL + if (any(mappings[["type"]] == "1-1")) { + i <- which(mappings[["type"]] == "1-1") + tmp <- mat[mappings[["x"]][i],,drop=FALSE] + rownames(tmp) <- mappings[["y"]][i] + rslt <- rbind(rslt, tmp) + } + if (any(mappings[["type"]] == "1-many")) { + i <- which(mappings[["type"]] == "1-many") + tmp <- mat[mappings[["x"]][i],,drop=FALSE] + rownames(tmp) <- mappings[["y"]][i] + rslt <- rbind(rslt, tmp) + } + if (any(mappings[["type"]] == "many-1")) { + i <- which(mappings[["type"]] == "many-1") + i <- split(mappings[["x"]][i], mappings[["y"]][i]) + tmp <- switch(method, + sum=sapply(i, function(j) colSums(mat[j,,drop=FALSE], na.rm=TRUE)), + max=sapply(i, function(j) { x <- mat[j,,drop=FALSE] ; x <- x[order(-rowSums(x, na.rm=TRUE)),,drop=FALSE] ; x[1,] }), + maxabs=sapply(i, function(j) { x <- mat[j,,drop=FALSE] ; x <- x[order(-rowSums(abs(x), na.rm=TRUE)),,drop=FALSE] ; x[1,] }) + ) + if (!is.matrix(x)) tmp <- matrix(tmp, ncol=1, dimnames=list(names(i), colnames(mat))) + rslt <- rbind(rslt, tmp) + } + + rslt +} + +#' Gets a TxDb/EnsDb object +#' +#' The TxDb/EnsDb object can be obtained from different inputs +#' - An existing TxDb or EnsDb object, in this case the function is only a pass-through, +#' - The name of TxDb/EnsDb package, possibly qualified with the object name in the environment, or +#' - The name of a GTF/GFF file, or +#' - An existing GRanges object +#' +#' @param tx_obj TxDb/EnsDb, GRanges, filename or package/object name +#' +#' @return TxDb/EnsDb object +#' @export +#' +#' @examples +get_tx_object <- function(tx_obj, verbose=FALSE) { + if (missing(tx_obj) || is.null(tx_obj)) + stop("Missing features description object") + if (is.character(tx_obj) && length(tx_obj)==1 && !is.na(tx_obj) && tx_obj!="") { + if (file.exists(tx_obj)) { + if (verbose) cat("Taking features from GTF/GTF file ", tx_obj) + tx_obj <- GenomicFeatures::makeTxDbFromGFF(tx_obj) + } else { + if (grepl("::", tx_obj)) { + tx_obj <- getFromNamespace(sub("^.+::", "", tx_obj), ns=sub("::.+$", "", tx_obj)) + } else { + tx_obj <- getFromNamespace(tx_obj, ns=tx_obj) + } + } + } else { + if (is(tx_obj, "GRanges")) tx_obj <- GenomicFeatures::makeTxDbFromGRanges(tx_obj) + } + if (!(is(tx_obj, "TxDb") || is(tx_obj, "EnsDb"))) + stop("Illegal features description object") + tx_obj +} + +#' Gets a gene id mapping table +#' +#' The mapping table contains gene identifiers from HGNC (SYMBOL), ENSEMBL & NCBI (ENTREZ_ID). +#' The mapping table has no missing identifier, and no duplicate rows. +#' All ENTREZ_ID are numbers coded as characters. +#' +#' Several type of inputs are possible: +#' - An existing orgDb object, +#' - The name of an orgDb package, possibly qualified with the object name in the environment, or +#' - A tab-delimited file, containined the columns "SYMBOL", "ENSEMBL" and "ENTREZ_ID". +#' To enable the possibility to use genome-nexus files, a file with column names +#' "hgnc_symbol", "ensembl_canonical_gene", "entrez_gene_id" is also allowed. +#' +#' @param org_obj orgDb, mapping id filename or package/object name +#' +#' @return gene id mapping table with columns SYMBOL, ENSEMBL & ENTREZ_ID +#' @export +#' +#' @examples +get_id_mappings <- function(org_obj, verbose=FALSE) { + if (missing(org_obj) || is.null(org_obj)) + stop("Missing organism description object") + if (is(org_obj, "OrgDb")) { + if (verbose) cat("Gene id mappings taken from Bioconductor object") + id_mappings <- AnnotationDbi::select( + org_obj, keytype=pipeline_id, columns=c("ENSEMBL", "SYMBOL", "ENTREZ_ID"), + keys=AnnotationDbi::keys(org_obj, keytype=pipeline_id) + ) + } else { + if (!is.character(org_obj) || length(org_obj)!=1 || is.na(org_obj) || org_obj=="") + stop("Illegal organism description") + if (file.exists(org_obj)) { + if (verbose) cat("Gene id mappings taken from file ", org_obj) + id_mappings <- read.table(org_obj, sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE, quote="", comment="") + if (all(c("hgnc_symbol", "ensembl_canonical_gene", "entrez_gene_id") %in% colnames(id_mappings))) + id_mappings <- id_mappings %>% + dplyr::select(ENSEMBL=ensembl_canonical_gene, SYMBOL=hgnc_symbol, ENTREZ_ID=entrez_gene_id) + stopifnot(all(c("ENSEMBL", "SYMBOL", "ENTREZ_ID") %in% colnames(id_mappings))) + id_mappings <- id_mappings[,c("ENSEMBL", "SYMBOL", "ENTREZ_ID")] + } else { + if (grepl("::", org_obj)) { + org_obj <- getFromNamespace(sub("^.+::", "", org_obj), ns=sub("::.+$", "", org_obj)) + } else { + org_obj <- getFromNamespace(org_obj, ns=org_obj) + } + id_mappings <- AnnotationDbi::select( + org_obj, keytype=pipeline_id, columns=c("ENSEMBL", "SYMBOL", "ENTREZ_ID"), + keys=AnnotationDbi::keys(org_obj, keytype=pipeline_id) + ) + } + } + id_mappings <- id_mappings %>% + dplyr::select(ENSEMBL, SYMBOL, ENTREZ_ID) %>% + dplyr::mutate(ENTREZ_ID=as.character(ENTREZ_ID)) %>% + dplyr::filter(!is.na(ENSEMBL) & ENSEMBL!="") %>% + dplyr::filter(!is.na(SYMBOL) & SYMBOL!="") %>% + dplyr::filter(!is.na(ENTREZ_ID) & ENTREZ_ID!="" & grepl("^[0-9]+$", ENTREZ_ID)) %>% + dplyr::distinct() + + id_mappings +} + +#' Create table of mappings between two sets of ids +#' +#' Creates a complete mapping between two sets of ids (x & y) of the same length. +#' The mappings are given a type (1-1, 1-many, many-1 & many-many), and +#' a group identifier, so that the mappings of all y ids corresponding to +#' a single x id in a 1-many relationship are given the same group number. +#' Missing values and duplicate entries in the input are ignored. +#' +#' The function creates a data frame containing all mappings between ids in +#' set x and ids in set y. These mappings are given a type (1-1, 1-many, +#' many-1 and many-many), and the original mappings are completed to include +#' all mappings between an x and a y which are connected by some path. +#' For example, if the x and y inputs are \code{x = c("x1", "x2", "x2")} and +#' \code{y = c("y1", "y1", "y2")}, which describe that id x1 is mapped to y1, +#' x2 is mapped to y1 and y2, then in the output, x1 will be mapped to y2. +#' A single group id will be assigned to the 4 connections (x1 to y1, x1 to y2, +#' x2 to y1 and x2 to y2). +#' If \code{haveIndex = TRUE}, the function will also create a column which +#' contains the indices of the original mappings in the input vectors. In the +#' example above, the index column will be 1 for x1 to y1, 2 for x2 to y1, +#' 3 for x2 to y2 and NA for x1 to y2, as the latter is not present in the +#' input. +#' Note that the index column is a column of lists, as it will report all +#' occurences of the original mapping, which might appear several times. +#' The missing mappings (which have NAs in either x or y input vectors) are +#' discarded. +#' +#' @param x vector of ids +#' @param y vector of ids +#' @param haveIndex return index of mapping in original vectors +#' @param verbose output progress messages +#' @param keepBlanks allow the empty string as valid ID +#' +#' @return data.frame with columns x (the first id), y (the second id), +#' type (the mapping type, 1-1, 1-many, many-1 or many-many), +#' group (an integer grouping id pairs), and optionally index, a +#' pointer to the mapping's position in the initial input. If the +#' mapping is not in the original input (i.e. it has been created +#' because of other connections between x and y ids), then the value +#' of the index is NA. +#' @export +#' +#' @examples{ +#' map_between_two_ids(c("x1", "x2", "x2", "x3", "x4", "x5", "x6", "x6"), +#' c("y1", "y1", "y2", "y3", "y4", "y4", "y5", "y6")) +#' } +map_between_two_ids <- function( x, y, haveIndex=TRUE, verbose=TRUE, keepBlanks=FALSE ) { + # Cleanup input + if( missing(x) || missing(y) || + is.null( x ) || is.null( y ) || length( x ) < 1 || + length( x ) != length( y ) ) + stop( "Missing arguments" ) + if( verbose ) cat( "Starting grouping", length( x ), "elements\n" ) + df <- unique( cbind( x=as.character( x ), y=as.character( y ) ) ) + rownames( df ) <- NULL + df <- df[rowSums( is.na( df ) )==0,] + if( ! keepBlanks ) df <- df[rowSums( df == "" )==0,] + if( verbose ) cat( "Number of complete pairs:", nrow( df ), "\n" ) + if( nrow( df ) == 0 ) return( NULL ) + + # Split by x and y columns + ys_from_x <- split( df[,"y"], df[,"x"] ) + xs_from_y <- split( df[,"x"], df[,"y"] ) + one_y_from_x <- unlist( ys_from_x[lengths(ys_from_x) == 1] ) + many_ys_from_x <- ys_from_x[lengths(ys_from_x) > 1] + one_x_from_y <- unlist( xs_from_y[sapply( xs_from_y, length )==1] ) + many_xs_from_y <- xs_from_y[sapply( xs_from_y, length )>1] + + igroup <- 0 + # 1-1 mappings: those in one_y_from_x that also are in one_x_from_y + rslt <- data.frame( group=as.numeric( c() ), + x=as.character( c() ), y=as.character( c() ), + type=as.character(), + stringsAsFactors=FALSE ) + if( length( one_y_from_x ) > 0 && length( one_x_from_y ) > 0 ) { + tmp <- one_y_from_x[names( one_y_from_x ) %in% one_x_from_y] + if (length(tmp)>0) { + tmp <- data.frame( group=igroup+(1:length( tmp )), + x=names( tmp ), y=tmp, + type="1-1", + stringsAsFactors=FALSE ) + rownames( tmp ) <- NULL + igroup <- nrow(tmp) + rslt <- rbind(rslt, tmp) + + # Remove 1-1 mappings from single splits + one_y_from_x <- one_y_from_x[!(one_y_from_x %in% tmp$y)] + one_x_from_y <- one_x_from_y[!(one_x_from_y %in% tmp$x)] + } + if( verbose ) cat( "Number of 1-1 pairs:", nrow( tmp ), "\n" ) + } + + # many-1 mappings: each y has many xs (only xs which map to a single y must be considered) + if( length( one_y_from_x ) > 0 && length( many_xs_from_y ) > 0 ) { + many_to_1_x <- names( one_y_from_x ) + many_to_one <- many_xs_from_y[sapply( many_xs_from_y, function( y ) all( y %in% many_to_1_x ) )] + n <- 0 + if (length(many_to_one) > 0) { + tmp <- data.frame( group=igroup + rep( (1:length( many_to_one )), lengths( many_to_one ) ), + x=unlist(many_to_one), y=rep(names(many_to_one), lengths(many_to_one)), + type="many-1", + stringsAsFactors=FALSE ) + rownames( tmp ) <- NULL + rslt <- rbind( rslt, tmp ) + n <- nrow(tmp) + igroup <- igroup + length(many_to_one) + + # Remove many-1 mappings from single splits + many_xs_from_y <- many_xs_from_y[!(names( many_xs_from_y ) %in% names( many_to_one ))] + one_y_from_x <- one_y_from_x[!(names(one_y_from_x) %in% many_to_1_x)] + } + if( verbose ) cat( "Number of many-1 pairs:", n, "\n" ) + } + + # 1-many mappings: each x has many ys (only ys that map to a single xmust be considered) + if( length( one_x_from_y ) > 0 && length( many_ys_from_x ) > 0 ) { + one_to_many_y <- names( one_x_from_y ) + one_to_many <- many_ys_from_x[sapply( many_ys_from_x, function( x ) all( x %in% one_to_many_y ) )] + n <- 0 + if (length(one_to_many) > 0) { + tmp <- data.frame( group=igroup + rep( (1:length( one_to_many )), lengths( one_to_many ) ), + x=rep(names(one_to_many), lengths(one_to_many)), y=unlist(one_to_many), + type="1-many", + stringsAsFactors=FALSE ) + rownames( tmp ) <- NULL + rslt <- rbind( rslt, tmp ) + n <- nrow(tmp) + igroup <- igroup + length(one_to_many) + + many_ys_from_x <- many_ys_from_x[!(names( many_ys_from_x ) %in% names( one_to_many ))] + one_x_from_y <- one_x_from_y[!(names(one_x_from_y) %in% one_to_many_y)] + } + if( verbose ) cat( "Number of 1-many pairs:", n, "\n" ) + } + + # many-many mappings + if( length( many_ys_from_x )>0 && length(many_xs_from_y)>0) { + # Create a matrix with all remaining connections + m <- rbind( data.frame(x=rep(names(many_ys_from_x), lengths(many_ys_from_x)), y=unlist(many_ys_from_x), + stringsAsFactors=FALSE), + data.frame(x=unlist(many_xs_from_y), y=rep(names(many_xs_from_y), lengths(many_xs_from_y)), + stringsAsFactors=FALSE), + data.frame(x=one_x_from_y, y=names(one_x_from_y), stringsAsFactors=FALSE), + data.frame(x=names(one_y_from_x), y=one_y_from_x, stringsAsFactors=FALSE) + ) + m <- as.matrix( unique( m ) ) + if( verbose ) cat( "Number of many-many pairs:", nrow( m ), "\n" ) + if( verbose ) cat( "Finding groups...\n" ) + + # Get the connected components for this graph + m[,1] <- paste( "x", m[,1], sep="\t" ) + m[,2] <- paste( "y", m[,2], sep="\t" ) + g <- igraph::graph_from_edgelist( m, directed=FALSE ) + cl <- igraph::components( g, mode="strong" ) + i <- split( names( cl$membership ), cl$membership ) + assertthat::assert_that(min(lengths(i))>3) + if( verbose ) cat( "Number of many-many groups:", length( i ), "\n" ) + + # Transform so that each group in i has 2 lists which contain the x & y items + i <- lapply( i, function( ii ) matrix( unlist( stringr::str_split( ii, "\t" ) ), nrow=2 ) ) + i <- lapply( i, function( ii ) split( ii[2,], ii[1,] ) ) + + # Build the dataframe for all, filling it with all combinations of x & y + n <- sum( sapply( i, function( ii ) length( ii$x )*length( ii$y ) ) ) + tmp <- data.frame( group=rep( NA, n ), x=rep( NA, n ), y=rep( NA, n ), type="many-many", + stringsAsFactors=FALSE) + k <- 0 + for( j in names( i ) ) { + igroup <- igroup+1 + nx <- length( i[[j]]$x ) + ny <- length( i[[j]]$y ) + tmp[k+(1:(nx*ny)),"group"] <- igroup + tmp[k+(1:(nx*ny)),"x"] <- rep( i[[j]]$x, each=ny ) + tmp[k+(1:(nx*ny)),"y"] <- rep( i[[j]]$y, nx ) + k <- k + nx*ny + } + rslt <- rbind( rslt, tmp ) + } + + # Show the mappings that were actually in the input + if( haveIndex ) { + i <- split( 1:length( x ), paste( as.character( x ), as.character( y ), sep="\t" ) ) + j <- match( paste( as.character( rslt$x ), as.character( rslt$y ), sep="\t" ), names( i ) ) + rslt$index <- c() + rslt$index[!is.na( j )] <- i[j[!is.na( j )]] + assertthat::assert_that(all(!is.na(rslt$index)[rslt$type!="many-many"])) + } + + rslt +} diff --git a/snappy_wrappers/wrappers/cbioportal/merge_tables/environment.yaml b/snappy_wrappers/wrappers/cbioportal/merge_tables/environment.yaml index 6e3bfe61c..1f257fe3a 100644 --- a/snappy_wrappers/wrappers/cbioportal/merge_tables/environment.yaml +++ b/snappy_wrappers/wrappers/cbioportal/merge_tables/environment.yaml @@ -1,7 +1,14 @@ +name: merge_tables + channels: -- bioconda - conda-forge -- anaconda -dependencies: -- pandas +- bioconda +- r +dependencies: +- r-base +- r-tidyverse +- r-igraph +- bioconductor-genomicranges +- bioconductor-genomicfeatures +- bioconductor-deseq2 diff --git a/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R b/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R new file mode 100644 index 000000000..8d1a26ddf --- /dev/null +++ b/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R @@ -0,0 +1,162 @@ +require(magrittr) + +#' Read & merge sample files into cBioPortal gene-based data table. +#' +#' Used for expression tables, log2 CNA, pseudo-Gistic table. +#' +#' @param fns named list or vector of sample files, with sample ids as names +#' @param mappings mapping table between feature ids (must contain ENSEMBL, SYMBOL & ENTREZ_ID columns) +#' @param type type of data to merge +#' @param args named list of additional arguments required to process the data before exporting +#' @param remove_feature_version remove the trailing "." in the feature id (useful for GENCODE) +#' +#' @example +merge_tables <- function(fns, mappings, type=c("log2", "gistic", "segment", "expression"), args=list(), remove_feature_version=TRUE) { + type <- match.arg(type) + + if (missing(fns) || is.null(fns)) + stop("Missing list of sample files") + if (is.list(fns)) { + stopifnot(all(lengths(fns) == 1)) + fns <- unlist(fns) + } + if (!is.character(fns) || any(is.na(fns)) || any(fns=="")) + stop("Missing at least one sample filename") + if (is.null(names(fns)) || any(is.na(names(fns))) || any(names(fns)=="")) + stop("Missing at least one sample id") + + if (type == "segment") return(merge_segments(fns)) + + if (missing(mappings) || is.null(mappings) || !is.character(mappings) || length(mappings)!=1 || is.na(mappings) || mappings=="") + stop("Missing or illegal gene id mappings filename") + mappings <- get_id_mappings(mappings, verbose=TRUE) + + if (type == "expression") { + stopifnot(all(c("pipeline_id", "tx_obj") %in% names(args))) + counts <- read_sample_files(fns, featureCol="V1", valueCol="V2", header=FALSE) + tmp <- compute_rpkm(counts, tx_obj=args$tx_obj, verbose=TRUE) + method <- "sum" + } + + if (type == "gistic") { + stopifnot(all(c("pipeline_id", "amplification") %in% names(args))) + # Copy numbers (in "cn" column) are transformed into (pseudo-) gistic codes: + # 0: Deep deletion, 1: heterozygous deletion, 2: copy number neutral, 3: gain, 4: amplification + # In https://doi.org/10.1038/s41586-022-04738-6, the amplification is defined as + # copy number greater or equal to 9 copies (args$amplification = 9). + args$amplification <- as.numeric(args$amplification) + cn <- read_sample_files(fns, args$pipeline_id, "cn") + cn[args$amplification<=cn] <- args$amplification + cn[20,,drop=FALSE] + if (nrow(counts) == 0) + stop("No feature with counts") + counts <- counts[,colSums(is.na(counts))==0,drop=FALSE] + if (ncol(counts) == 0) + stop("No sample without missing value") + + # Append the gene locii to the counts in dds object + if (verbose) cat("Create DESeq2 object ... ") + genes <- GenomicFeatures::exonsBy(tx_obj, "gene") + genes <- genes[names(genes) %in% rownames(counts)] + counts <- counts[names(genes),] + donors <- data.frame(Donor=colnames(counts), stringsAsFactors=FALSE) + dds <- DESeq2::DESeqDataSetFromMatrix(counts, colData=donors, design=as.formula("~ 1"), rowRanges=genes) + if (verbose) cat("Done\n") + + # Compute FPKMs + if (verbose) cat("Compute FPKM ... ") + dds <- DESeq2::estimateSizeFactors(dds) + FPKM <- DESeq2::fpkm(dds, robust=TRUE) + if (verbose) cat("Done\n") + + FPKM +} diff --git a/snappy_wrappers/wrappers/cbioportal/merge_tables/wrapper.py b/snappy_wrappers/wrappers/cbioportal/merge_tables/wrapper.py index 96de11288..b4e4d94b1 100644 --- a/snappy_wrappers/wrappers/cbioportal/merge_tables/wrapper.py +++ b/snappy_wrappers/wrappers/cbioportal/merge_tables/wrapper.py @@ -1,39 +1,68 @@ # -*- coding: utf-8 -*- """Wrapper for merging multiple tables in R on shared columns""" +import os -__author__ = "Clemens Messerschmidt " +from snakemake import shell -import re +__author__ = "Eric Blanc " -import pandas as pd +r_script = os.path.abspath(os.path.join(os.path.dirname(__file__), "script.R")) +helper_functions = os.path.join(os.path.dirname(r_script), "..", "helper_functions.R") -pattern = re.compile("(.+)-[DR]NA[0-9]+-(WES|WGS|mRNA_seq)[0-9]+$") +filenames = ", ".join(['"{}"="{}"'.format(str(k), str(v)) for k, v in snakemake.input.items()]) +extra_args = ", ".join( + ['"{}"="{}"'.format(str(k), str(v)) for k, v in snakemake.params["extra_args"].items()] +) +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step] -def readTable(fn, dataint=False): - df = pd.read_csv(fn, sep="\t", header=0) - df = df.dropna() - df = df.astype({"Entrez_Gene_Id": "str"}) - df = df.groupby(["Hugo_Symbol", "Entrez_Gene_Id"]).median() - df = df.reset_index() - # WARNING- pandas rounds towards 0, not to nearest int - if dataint: - df = df.astype({df.columns[2]: "int32"}) - return df +shell( + r""" +set -x +# Write files for reproducibility ----------------------------------------------------------------- -joined = None -for fn in snakemake.input: - df = readTable(fn, dataint=(snakemake.params.datatype == "int")) - if joined is None: - joined = df - else: - joined = pd.merge(joined, df, on=["Hugo_Symbol", "Entrez_Gene_Id"], how="outer") +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +pushd $(dirname {snakemake.log.conda_list}) ; md5sum $(basename {snakemake.log.conda_list}) > $(basename {snakemake.log.conda_list_md5}) ; popd +pushd $(dirname {snakemake.log.conda_info}) ; md5sum $(basename {snakemake.log.conda_info}) > $(basename {snakemake.log.conda_info_md5}) ; popd -joined.columns = [pattern.sub("\\1", x) for x in joined.columns] +# Also pipe stderr to log file -------------------------------------------------------------------- -if snakemake.params.datatype == "int": - joined.to_csv(str(snakemake.output), sep="\t", na_rep="NA", index=False, float_format="%.0f") -else: - joined.to_csv(str(snakemake.output), sep="\t", na_rep="NA", index=False) +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Create auto-cleaned temporary directory --------------------------------------------------------- + +export TMPDIR=$(mktemp -d) +trap "rm -rf $TMPDIR" EXIT + +# Run the R script -------------------------------------------------------------------------------- + +R --vanilla --slave << __EOF +source("{helper_functions}") +source("{r_script}") +write.table( + merge_tables(list({filenames}), mappings="{config[path_gene_id_mappings]}", type="{snakemake.params[action_type]}", args=list({extra_args})), + file="{snakemake.output}", sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE +) +__EOF +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +sleep 1s # try to wait for log file flush +pushd $(dirname {snakemake.log.conda_info}) ; md5sum $(basename {snakemake.log.log}) > $(basename {snakemake.log.log_md5}) ; popd +""" +) diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_clinical_patient.txt b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_clinical_patient.txt index 058e28d89..c9721aaac 100644 --- a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_clinical_patient.txt +++ b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_clinical_patient.txt @@ -1,4 +1,4 @@ -cancer_study_identifier: __CANCER_STUDY_IDENTIFIER__ +cancer_study_identifier: {cancer_study_id} genetic_alteration_type: CLINICAL datatype: PATIENT_ATTRIBUTES -data_filename: data_clinical_patients.txt +data_filename: data_clinical_patient.txt diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_clinical_sample.txt b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_clinical_sample.txt index 56600957f..1960d4df9 100644 --- a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_clinical_sample.txt +++ b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_clinical_sample.txt @@ -1,4 +1,4 @@ -cancer_study_identifier: __CANCER_STUDY_IDENTIFIER__ +cancer_study_identifier: {cancer_study_id} genetic_alteration_type: CLINICAL datatype: SAMPLE_ATTRIBUTES -data_filename: data_clinical_samples.txt +data_filename: data_clinical_sample.txt diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_CNA_gistic.txt b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_cna_gistic.txt similarity index 79% rename from snappy_wrappers/wrappers/cbioportal/meta_files/meta_CNA_gistic.txt rename to snappy_wrappers/wrappers/cbioportal/meta_files/meta_cna_gistic.txt index 4e6aae540..5e4a2d1ec 100644 --- a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_CNA_gistic.txt +++ b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_cna_gistic.txt @@ -1,8 +1,8 @@ -cancer_study_identifier: __CANCER_STUDY_IDENTIFIER__ +cancer_study_identifier: {cancer_study_id} genetic_alteration_type: COPY_NUMBER_ALTERATION datatype: DISCRETE stable_id: cna show_profile_in_analysis_tab: true profile_name: Pseudo-GISTIC computation profile_description: Putative copy-number from CNVkit. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. -data_filename: data_CNA_gistic.txt +data_filename: data_cna_gistic.txt diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_CNA_log2.txt b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_cna_log2.txt similarity index 71% rename from snappy_wrappers/wrappers/cbioportal/meta_files/meta_CNA_log2.txt rename to snappy_wrappers/wrappers/cbioportal/meta_files/meta_cna_log2.txt index 6e08ef1e6..033962f37 100644 --- a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_CNA_log2.txt +++ b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_cna_log2.txt @@ -1,8 +1,8 @@ -cancer_study_identifier: __CANCER_STUDY_IDENTIFIER__ +cancer_study_identifier: {cancer_study_id} genetic_alteration_type: COPY_NUMBER_ALTERATION datatype: LOG2-VALUE stable_id: log2CNA show_profile_in_analysis_tab: false profile_name: Log2 copy-number values profile_description: Log2 copy-number from CopywriteR -data_filename: data_CNA_log2.txt +data_filename: data_cna_log2.txt diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_expression.txt b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_expression.txt new file mode 100644 index 000000000..e6d5d0b5a --- /dev/null +++ b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_expression.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: {cancer_study_id} +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: rna_seq_mrna +show_profile_in_analysis_tab: true +profile_name: mRNA expression FPKMs +profile_description: Expression levels FPKMs +data_filename: data_expression.txt diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_expression_zscores.txt b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_expression_zscores.txt deleted file mode 100644 index 888f1a0d7..000000000 --- a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_expression_zscores.txt +++ /dev/null @@ -1,8 +0,0 @@ -cancer_study_identifier: __CANCER_STUDY_IDENTIFIER__ -genetic_alteration_type: MRNA_EXPRESSION -datatype: Z-SCORE -stable_id: rna_seq_mrna_median_Zscores -show_profile_in_analysis_tab: true -profile_name: mRNA expression z-scores -profile_description: Expression levels z-scores -data_filename: data_expression_zscores.txt diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_mutation_extended.txt b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_mutation_extended.txt index 2b6268856..2acb5919e 100644 --- a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_mutation_extended.txt +++ b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_mutation_extended.txt @@ -1,4 +1,4 @@ -cancer_study_identifier: __CANCER_STUDY_IDENTIFIER__ +cancer_study_identifier: {cancer_study_id} genetic_alteration_type: MUTATION_EXTENDED datatype: MAF stable_id: mutations diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_segment.txt b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_segment.txt index c680158f3..aee0c20aa 100644 --- a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_segment.txt +++ b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_segment.txt @@ -1,6 +1,6 @@ -cancer_study_identifier: __CANCER_STUDY_IDENTIFIER__ +cancer_study_identifier: {cancer_study_id} genetic_alteration_type: COPY_NUMBER_ALTERATION datatype: SEG -reference_genome_id: hg19 +reference_genome_id: {reference_genome} description: Somatic CNA data data_filename: data_segment.txt diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/meta_study.txt b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_study.txt new file mode 100644 index 000000000..3b8636cff --- /dev/null +++ b/snappy_wrappers/wrappers/cbioportal/meta_files/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: {type_of_cancer} +cancer_study_identifier: {cancer_study_id} +name: {study_name} +short_name: {study_name_short} +description: {study_description} +add_global_case_list: true +reference_genome: {reference_genome} diff --git a/snappy_wrappers/wrappers/cbioportal/meta_files/wrapper.py b/snappy_wrappers/wrappers/cbioportal/meta_files/wrapper.py index f54f976a5..7438944d6 100644 --- a/snappy_wrappers/wrappers/cbioportal/meta_files/wrapper.py +++ b/snappy_wrappers/wrappers/cbioportal/meta_files/wrapper.py @@ -3,15 +3,16 @@ See https://github.com/cBioPortal/cbioportal/blob/master/docs/File-Formats.md#clinical-data """ -from glob import glob import os -target_dir = "work/upload" source_dir = os.path.abspath(os.path.dirname(__file__)) -study_id = snakemake.config["step_config"]["cbioportal_export"]["cancer_study_id"] # For each template, replace study_id and write to output in work dir -for tpl in glob(os.path.join(source_dir, "meta*.txt")): - with open(tpl) as infile, open(os.path.join(target_dir, os.path.basename(tpl)), "w") as outfile: +for fn in snakemake.output: + gn = os.path.join(source_dir, os.path.basename(fn)) + assert os.path.exists(gn) + with open(gn, "rt") as infile, open(fn, "wt") as outfile: for line in infile: - outfile.write(line.replace("__CANCER_STUDY_IDENTIFIER__", study_id)) + outfile.write( + line.format(**snakemake.config["step_config"]["cbioportal_export"]["study"]) + ) diff --git a/snappy_wrappers/wrappers/cbioportal/plot_expression_distribution/environment.yaml b/snappy_wrappers/wrappers/cbioportal/plot_expression_distribution/environment.yaml deleted file mode 100644 index 5c44fa731..000000000 --- a/snappy_wrappers/wrappers/cbioportal/plot_expression_distribution/environment.yaml +++ /dev/null @@ -1,9 +0,0 @@ -channels: -- bioconda -- conda-forge -- anaconda -dependencies: -- r -- r-dplyr -- bioconductor-gsva -- bioconductor-cqn diff --git a/snappy_wrappers/wrappers/cbioportal/plot_expression_distribution/wrapper.py b/snappy_wrappers/wrappers/cbioportal/plot_expression_distribution/wrapper.py deleted file mode 100644 index 7b9aa2662..000000000 --- a/snappy_wrappers/wrappers/cbioportal/plot_expression_distribution/wrapper.py +++ /dev/null @@ -1,77 +0,0 @@ -# -*- coding: utf-8 -*- -"""Wrapper for computing expression signatures from counts""" - -import os.path - -from snakemake import shell - -if len(snakemake.output.pdf) == 1: - snakemake.output.pdf = snakemake.output.pdf[0] -else: - raise - -sample_tpl = os.path.basename(os.path.dirname(os.path.dirname(snakemake.output.pdf))) -sample_dir = os.path.dirname(os.path.dirname(snakemake.output.pdf)) - -__author__ = "Clemens Messerschmidt " - -shell.executable("/bin/bash") - -shell( - r""" -set -x - -export TMPDIR=$(mktemp -d) -trap "rm -rf $TMPDIR" EXIT - -# Also pipe stderr to log file -if [[ -n "{snakemake.log}" ]]; then - if [[ "$(set +e; tty; set -e)" != "" ]]; then - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - exec 2> >(tee -a "{snakemake.log}" >&2) - else - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - echo "No tty, logging disabled" >"{snakemake.log}" - fi -fi - -# ------------------------------------------------------------------------------------------------- -# Write helper script and call R -# -cat <<"EOF" > $TMPDIR/compute_signatures.R -library( magrittr ) -library( methods ) # https://github.com/tidyverse/broom/issues/67 - -gene_exp = read.delim("{snakemake.input.tsv}", stringsAsFactors=FALSE) - -# genes of interest -# TODO make configurable -goi = read.table( - "/fast/groups/cubi/projects/2016-09-27_DKTK/pipeline/CLEMENS_misc/Vogelstein/Vogelstein_gene_names.txt", - quote="\"", comment.char="") - -sample = make.names("{sample_tpl}") -idx = which(sample == names(gene_exp)) - -m = as.matrix(gene_exp) -m = m[rownames(m) %in% goi$V1, ] - -print(dim(m)) - -dir.create("{sample_dir}") -pdf("{snakemake.output.pdf}") - -for (i in 1:nrow(m)) {{ - if (is.na(sum(m[i, ]))) continue - plot(density(m[i, ]), main=rownames(m)[i]) - abline(v=m[i, sample], col=2, lwd=3) -}} -dev.off() - -warnings() -sessionInfo() -EOF - -Rscript --vanilla $TMPDIR/compute_signatures.R -""" -) diff --git a/snappy_wrappers/wrappers/cbioportal/rank_expression/environment.yaml b/snappy_wrappers/wrappers/cbioportal/rank_expression/environment.yaml deleted file mode 100644 index f01afca99..000000000 --- a/snappy_wrappers/wrappers/cbioportal/rank_expression/environment.yaml +++ /dev/null @@ -1,12 +0,0 @@ -channels: -- bioconda -- conda-forge -- anaconda -dependencies: -- r -- r-dplyr -- bioconductor-edgeR -- bioconductor-DESeq2 -- bioconductor-org.hs.eg.db -- bioconductor-txdb.hsapiens.ucsc.hg19.knowngene -- openblas diff --git a/snappy_wrappers/wrappers/cbioportal/rank_expression/wrapper.py b/snappy_wrappers/wrappers/cbioportal/rank_expression/wrapper.py deleted file mode 100644 index a728f50c8..000000000 --- a/snappy_wrappers/wrappers/cbioportal/rank_expression/wrapper.py +++ /dev/null @@ -1,76 +0,0 @@ -# -*- coding: utf-8 -*- -"""Wrapper for computing expression values (RPKM) from counts""" - -import os.path - -from snakemake import shell - -sample_tpl = os.path.basename(os.path.dirname(os.path.dirname(snakemake.output.tsv))) - -__author__ = "Clemens Messerschmidt " - -shell.executable("/bin/bash") - -shell( - r""" -set -x - -export TMPDIR=$(mktemp -d) -trap "rm -rf $TMPDIR" EXIT - -# Also pipe stderr to log file -if [[ -n "{snakemake.log}" ]]; then - if [[ "$(set +e; tty; set -e)" != "" ]]; then - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - exec 2> >(tee -a "{snakemake.log}" >&2) - else - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - echo "No tty, logging disabled" >"{snakemake.log}" - fi -fi - -# ------------------------------------------------------------------------------------------------- -# Write helper script and call R -# -cat <<"EOF" > $TMPDIR/compute_zscores.R -library( magrittr ) -library( methods ) # https://github.com/tidyverse/broom/issues/67 - -gene_exp = read.delim("{snakemake.input.tsv}", stringsAsFactors=FALSE) - -# https://stackoverflow.com/a/36159165 -ranks = t(apply(-gene_exp, 1, rank)) - -zscores = t(apply(gene_exp, 1, scale)) - -sample = make.names("{sample_tpl}") -idx = which(sample == names(gene_exp)) - -res_df = cbind( - rownames(gene_exp), - zscores[ , idx], - log2(gene_exp[ , idx] + 0.001) - log2(apply(gene_exp, 1, median) + 0.001), - ranks[ , idx], - gene_exp[ , idx], - apply(gene_exp, 1, median), - apply(gene_exp, 1, max), - apply(gene_exp, 1, min)) - -colnames(res_df) = c("gene_symbol", - "z_score", - "logFC_to_cohort_median", - "cohort_rank", - "normalized_expression_in_sample", - "cohort_median", - "cohort_max", - "cohort_min") - -write.table(res_df, file = "{snakemake.output.tsv}", quote=F, row.names=F, sep="\t") - -warnings() -sessionInfo() -EOF - -Rscript --vanilla $TMPDIR/compute_zscores.R -""" -) diff --git a/snappy_wrappers/wrappers/cbioportal/rpkm_expression/environment.yaml b/snappy_wrappers/wrappers/cbioportal/rpkm_expression/environment.yaml deleted file mode 100644 index f01afca99..000000000 --- a/snappy_wrappers/wrappers/cbioportal/rpkm_expression/environment.yaml +++ /dev/null @@ -1,12 +0,0 @@ -channels: -- bioconda -- conda-forge -- anaconda -dependencies: -- r -- r-dplyr -- bioconductor-edgeR -- bioconductor-DESeq2 -- bioconductor-org.hs.eg.db -- bioconductor-txdb.hsapiens.ucsc.hg19.knowngene -- openblas diff --git a/snappy_wrappers/wrappers/cbioportal/rpkm_expression/scripts.R b/snappy_wrappers/wrappers/cbioportal/rpkm_expression/scripts.R deleted file mode 120000 index 87d0b3815..000000000 --- a/snappy_wrappers/wrappers/cbioportal/rpkm_expression/scripts.R +++ /dev/null @@ -1 +0,0 @@ -../scripts.R \ No newline at end of file diff --git a/snappy_wrappers/wrappers/cbioportal/rpkm_expression/wrapper.py b/snappy_wrappers/wrappers/cbioportal/rpkm_expression/wrapper.py deleted file mode 100644 index b63c4e889..000000000 --- a/snappy_wrappers/wrappers/cbioportal/rpkm_expression/wrapper.py +++ /dev/null @@ -1,50 +0,0 @@ -# -*- coding: utf-8 -*- -"""Wrapper for computing expression values (RPKM) from counts""" - -import os.path - -from snakemake import shell - -rcode = os.path.join(os.path.dirname(__file__), "scripts.R") - -__author__ = "Clemens Messerschmidt " - -shell.executable("/bin/bash") - -shell( - r""" -set -x - -export TMPDIR=$(mktemp -d) -trap "rm -rf $TMPDIR" EXIT - -# Also pipe stderr to log file -if [[ -n "{snakemake.log}" ]]; then - if [[ "$(set +e; tty; set -e)" != "" ]]; then - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - exec 2> >(tee -a "{snakemake.log}" >&2) - else - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - echo "No tty, logging disabled" >"{snakemake.log}" - fi -fi - -# ------------------------------------------------------------------------------------------------- -# Write helper script and call R -# -cat <<"EOF" > $TMPDIR/compute_rpkm.R -library( magrittr ) -library( methods ) # https://github.com/tidyverse/broom/issues/67 -source("{rcode}") - -mapping_df <- read.table("{snakemake.input.tsv}", sep="\t", header=1, stringsAsFactors=FALSE) -rpkm <- compute_rpkm(mapping_df) -write.table(rpkm, file="{snakemake.output.tsv}", sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE) - -warnings() -sessionInfo() -EOF - -Rscript --vanilla $TMPDIR/compute_rpkm.R -""" -) diff --git a/snappy_wrappers/wrappers/cbioportal/scripts.R b/snappy_wrappers/wrappers/cbioportal/scripts.R deleted file mode 100644 index a7a65b7c1..000000000 --- a/snappy_wrappers/wrappers/cbioportal/scripts.R +++ /dev/null @@ -1,496 +0,0 @@ -require(magrittr) - -#' Aggregates counts and computes RPKM -#' -#' The computation of RPKM is done using DESeq2::fpkm in robust mode (after library size estimation). -#' The gene lengths are estimated using the total span of all its exons, which will lead -#' to gene length over-estimation in most cases. -#' -#' @param df data frame describing expression counts & CNV gene calls files -#' @param count_input_format gene expression counts file format (only "feature_counts" supported) -#' @param tx_obj Bioconductor feature description object (human by default, either TxDb or EnsDb) -#' @param org_obj Bioconductor organism object (human by default) -#' @param pipeline_id type of ids used by the pipeline ("ENSEMBL" by default) -#' @param symbol_id Hugo_Symbol id name in org_obj ("SYMBOL" by default) -#' @param verbose show progress of the computation -#' -#' @return the RPKM data frame -#' @export -#' -#' @examples -compute_rpkm <- function(df, - count_input_format="feature_counts", - tx_obj=TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene, - org_obj=org.Hs.eg.db::org.Hs.eg.db, pipeline_id="ENSEMBL", symbol_id="SYMBOL", - verbose=FALSE) { - if (missing(df) || is.null(df) || - !is.data.frame(df) || nrow(df)<1 || - !all(c("ID", "count_filename", "gene_call_filename") %in% colnames(df))) - stop("Missing or illegal directory path") - if (any(is.na(df$ID) | df$ID=="") || any(duplicated(df$ID))) - stop("Illegal ID column") - if (is.null(count_input_format) || - !is.character(count_input_format) || length(count_input_format)!=1 || is.na(count_input_format)) - stop("Missing or illegal file format for gene expression counts") - count_input_format <- match.arg(count_input_format) - if (is.null(tx_obj) || !(is(tx_obj, "TxDb") || is(tx_obj, "EnsDb"))) - stop("Missing or illegal features description object") - if (is.null(org_obj) || !is(org_obj, "OrgDb")) - stop("Missing or illegal organism description object") - if (is.null(pipeline_id) || !is.character(pipeline_id) || length(pipeline_id)!=1 || is.na(pipeline_id) || - pipeline_id=="" || !(pipeline_id %in% AnnotationDbi::columns(org_obj))) - stop("Missing, illegal or unknown pipeline id type") - if (is.null(symbol_id) || !is.character(symbol_id) || length(symbol_id)!=1 || is.na(symbol_id) || - symbol_id=="" || !(symbol_id %in% AnnotationDbi::columns(org_obj))) - stop("Missing, illegal or unknown Hugo_Symbol id type") - - # Identify samples with expression files - has_expr <- !is.na(df$count_filename) & df$count_filename!="" & file.access(df$count_filename, mode=4)==0 - names(has_expr) <- as.character(df$ID) - if (!any(has_expr)) - stop("No valid gene expression count file") - - # Read counts counts - if (verbose) cat("Read expression counts ... ") - counts <- switch( - count_input_format, - feature_counts=read_featurecounts_files(df$count_filename[has_expr]) - ) - colnames(counts) <- df$ID[has_expr] - if (verbose) cat("Done\n") - - # Remove samples with no expression counts (all NA) - has_expr[colnames(counts)] <- has_expr[colnames(counts)] & (colSums(!is.na(counts))>0) - if (!any(has_expr)) - stop("No gene expression sample with valid expression counts") - counts <- counts[,colSums(!is.na(counts))>0,drop=FALSE] - - # Remap counts to ENTREZ gene ids - if (verbose) cat("Convert gene ids from ENSEMBL to ENTREZ ... ") - rownames(counts) <- sub("\\.[0-9]+$", "", rownames(counts)) - counts <- pipeline_to_entrez(counts, org_obj=org_obj, pipeline_id=pipeline_id) - if (verbose) cat("Done\n") - - # Append the gene locii to the counts in dds object - if (verbose) cat("Create DESeq2 object ... ") - genes <- GenomicFeatures::exonsBy(tx_obj, "gene") - genes <- genes[names(genes) %in% rownames(counts)] - counts <- counts[names(genes),] - donors <- data.frame(Donor=colnames(counts), stringsAsFactors=FALSE) - dds <- DESeq2::DESeqDataSetFromMatrix(counts, colData=donors, design=as.formula("~ 1"), rowRanges=genes) - if (verbose) cat("Done\n") - - # Compute FPKMs - if (verbose) cat("Compute FPKM ... ") - dds <- DESeq2::estimateSizeFactors(dds) - FPKM <- DESeq2::fpkm(dds, robust=TRUE) - if (verbose) cat("Done\n") - - # Make data frame with Hugo_Symbol, Entrez_Gene_Id and z-scores columns - if (verbose) cat("Add gene symbols ... ") - gene_names <- AnnotationDbi::select(org_obj, - keys=rownames(FPKM), - keytype="ENTREZID", - columns=c(symbol_id, "ENTREZID")) - if (is.null(gene_names) || !is.data.frame(gene_names) || nrow(gene_names)<1) - stop("Entrez_Gene_Id ids not found") - gene_names <- gene_names[!is.na(gene_names[[symbol_id]]) & !is.na(gene_names[["ENTREZID"]]),] - if (nrow(gene_names)==0) - stop("No valid mappings") - gene_names <- gene_names[,c(symbol_id, "ENTREZID")] - colnames(gene_names) <- c("Hugo_Symbol", "Entrez_Gene_Id") - - FPKM <- FPKM[rownames(FPKM) %in% as.character(gene_names$Entrez_Gene_Id),,drop=FALSE] - i <- match(rownames(FPKM), as.character(gene_names$Entrez_Gene_Id)) - FPKM <- data.frame(gene_names[i,], FPKM, stringsAsFactors=FALSE, check.names=FALSE) - rownames(FPKM) <- NULL - if (verbose) cat("Done\n") - - FPKM -} - -#' Aggregates counts and creates z-scores file -#' -#' Pipeline-implementation agnostic, location of files defined in the input data.frame -#' -#' @param df data frame describing expression counts & CNV gene calls files -#' @param count_input_format gene expression counts file format (only "feature_counts" supported) -#' @param gene_call_input_format CNV gene calls file format (only "cubi_pipeline" supported) -#' @param org_obj Bioconductor organism object (human by default) -#' @param pipeline_id type of ids used by the pipeline ("ENSEMBL" by default) -#' @param symbol_id Hugo_Symbol id name in org_obj ("SYMBOL" by default) -#' @param min_nb_diploid minimum number of diploid samples in order to compute z-scores (default 10) -#' @param verbose show progress of the computation -#' @param fast use vst instead of rlog to compute normalised expression -#' -#' @return the z_score data frame -#' @export -#' -#' @examples -compute_z_scores <- function(df, - count_input_format="feature_counts", - gene_call_input_format="cubi_pipeline", - org_obj=org.Hs.eg.db::org.Hs.eg.db, pipeline_id="ENSEMBL", symbol_id="SYMBOL", - min_nb_diploid=10, - verbose=FALSE, fast=FALSE) { - if (missing(df) || is.null(df) || - !is.data.frame(df) || nrow(df)<1 || - !all(c("ID", "count_filename", "gene_call_filename") %in% colnames(df))) - stop("Missing or illegal directory path") - if (any(is.na(df$ID) | df$ID=="") || any(duplicated(df$ID))) - stop("Illegal ID column") - if (is.null(count_input_format) || - !is.character(count_input_format) || length(count_input_format)!=1 || is.na(count_input_format)) - stop("Missing or illegal file format for gene expression counts") - count_input_format <- match.arg(count_input_format) - if (is.null(gene_call_input_format) || - !is.character(gene_call_input_format) || length(gene_call_input_format)!=1 || is.na(gene_call_input_format)) - stop("Missing or illegal file format for CNV gene calls") - gene_call_input_format <- match.arg(gene_call_input_format) - if (is.null(org_obj) || !is(org_obj, "OrgDb")) - stop("Missing or illegal organism description object") - if (is.null(pipeline_id) || !is.character(pipeline_id) || length(pipeline_id)!=1 || is.na(pipeline_id) || - pipeline_id=="" || !(pipeline_id %in% AnnotationDbi::columns(org_obj))) - stop("Missing, illegal or unknown pipeline id type") - if (is.null(symbol_id) || !is.character(symbol_id) || length(symbol_id)!=1 || is.na(symbol_id) || - symbol_id=="" || !(symbol_id %in% AnnotationDbi::columns(org_obj))) - stop("Missing, illegal or unknown Hugo_Symbol id type") - - # Identify samples with expression files - has_expr <- !is.na(df$count_filename) & df$count_filename!="" & file.access(df$count_filename, mode=4)==0 - names(has_expr) <- as.character(df$ID) - if (!any(has_expr)) - stop("No valid gene expression count file") - - # Read counts counts - if (verbose) cat("Read expression counts ... ") - counts <- switch( - count_input_format, - feature_counts=read_featurecounts_files(df$count_filename[has_expr]) - ) - colnames(counts) <- df$ID[has_expr] - if (verbose) cat("Done\n") - - # Remove samples with no expression counts (all NA) - has_expr[colnames(counts)] <- has_expr[colnames(counts)] & (colSums(!is.na(counts))>0) - if (!any(has_expr)) - stop("No gene expression sample with valid expression counts") - counts <- counts[,colSums(!is.na(counts))>0,drop=FALSE] - - # Remap counts to ENTREZ gene ids - if (verbose) cat("Convert gene ids from ENSEMBL to ENTREZ ... ") - rownames(counts) <- sub("\\.[0-9]+$", "", rownames(counts)) - counts <- pipeline_to_entrez(counts, org_obj=org_obj, pipeline_id=pipeline_id) - if (verbose) cat("Done\n") - - # Normalise counts - if (verbose) cat("Normalise expression ... ") - has_expr[colnames(counts)] <- has_expr[colnames(counts)] & (colSums(is.na(counts))==0) - counts <- counts[,colSums(is.na(counts))==0,drop=FALSE] # Required for DESeq2::DESeq - if (!any(has_expr)) - stop("No valid gene expression sample for normalisation") - expr <- normalise_counts(counts, verbose=verbose, fast=fast) - if (verbose) cat("Done\n") - - # Identify files with CNV gene calls and - has_cnv <- !is.na(df$gene_call_filename) & df$gene_call_filename!="" & file.access(df$gene_call_filename, mode=0)==0 - has_both <- has_expr & has_cnv - - cnv_calls <- NULL - if (any(has_both)) { - if (verbose) cat("Read CNV gene calls ... ") - cnv_calls <- switch( - gene_call_input_format, - cubi_pipeline=process_cnv_genes(df[has_both,] %>% dplyr::rename(filename=gene_call_filename)) - ) - rownames(cnv_calls) <- as.character(cnv_calls$Entrez_Gene_Id) - cnv_calls <- cnv_calls %>% dplyr::select(-Hugo_Symbol, -Entrez_Gene_Id) %>% as.matrix() - colnames(cnv_calls) <- df$ID[has_both] - if (verbose) cat("Done\n") - } - - # Compute z-scores (when no CNV calls are present, use all samples) - if (verbose) cat("Compute expression z-scores ... ") - z <- z_scores(expr, cnv_calls, min_nb_diploid=min_nb_diploid) - if (verbose) cat("Done\n") - - # Gene symbols from ENTREZ ids - if (verbose) cat("Add gene symbols ... ") - if (any(has_both)) { - gene_names <- process_cnv_genes(df[has_both,] %>% dplyr::rename(filename=gene_call_filename)) %>% - dplyr::select(Hugo_Symbol, Entrez_Gene_Id) - } else { - if (!all(c(symbol_id, "ENTREZID") %in% AnnotationDbi::columns(org_obj))) - stop("Missing/illegal organism database (OrgDb object)") - - gene_names <- AnnotationDbi::select(org_obj, - keys=rownames(z), - keytype="ENTREZID", - columns=c(symbol_id, "ENTREZID")) - if (is.null(gene_names) || !is.data.frame(gene_names) || nrow(gene_names)<1) - stop("Entrez_Gene_Id ids not found") - gene_names <- gene_names[!is.na(gene_names[[symbol_id]]) & !is.na(gene_names[["ENTREZID"]]),] - if (nrow(gene_names)==0) - stop("No valid mappings") - gene_names <- gene_names[,c(symbol_id, "ENTREZID")] - colnames(gene_names) <- c("Hugo_Symbol", "Entrez_Gene_Id") - } - if (verbose) cat("Done\n") - - # Make data frame with Hugo_Symbol, Entrez_Gene_Id and z-scores columns - z <- z[rownames(z) %in% as.character(gene_names$Entrez_Gene_Id),,drop=FALSE] - i <- match(rownames(z), as.character(gene_names$Entrez_Gene_Id)) - z <- data.frame(gene_names[i,], z, stringsAsFactors=FALSE, check.names=FALSE) - rownames(z) <- NULL - - z -} - -#' Compute gene expression z-scores from diploid samples -#' -#' @param norm_expr normalised expression matrix -#' @param cnv_calls matrix of calls (0 for diploid) -#' @param min_nb_diploid minimum number of diploid samples in order to compute z-scores (default 10) -#' -#' @return a matrix of z scores -#' @export -#' -#' @examples -z_scores <- function(norm_expr, cnv_call=NULL, min_nb_diploid=10) { - if (missing(norm_expr) || is.null(norm_expr) || - !is.matrix(norm_expr) || nrow(norm_expr)<1 || ncol(norm_expr)<1 || - !is.numeric(norm_expr) || any(is.na(norm_expr)) || - is.null(rownames(norm_expr)) || any(is.na(rownames(norm_expr))) || any(rownames(norm_expr)=="") || - is.null(colnames(norm_expr)) || any(is.na(colnames(norm_expr))) || any(colnames(norm_expr)=="")) - stop("Missing/illegal normalised expression matrix") - if (is.null(min_nb_diploid) || !is.numeric(min_nb_diploid) || length(min_nb_diploid)!=1 || - is.na(min_nb_diploid) || min_nb_diploid<0) - stop("Missing/illegal minimum number of diploid samples") - if (min_nb_diploid<3) min_nb_diploid <- 3 - - filter <- matrix(TRUE, nrow=nrow(norm_expr), ncol=ncol(norm_expr), dimnames=dimnames(norm_expr)) - - if (!is.null(cnv_call)) { - if (!is.matrix(cnv_call) || nrow(cnv_call)<1 || ncol(cnv_call)<1 || - is.null(rownames(cnv_call)) || any(is.na(rownames(cnv_call))) || any(rownames(cnv_call)=="") || - is.null(colnames(cnv_call)) || any(is.na(colnames(cnv_call))) || any(colnames(cnv_call)=="")) - stop("Illegal gene-based copy-number matrix") - cnv_call <- !is.na(cnv_call) & cnv_call==0 - cnv_call <- cnv_call[rownames(cnv_call) %in% rownames(norm_expr),colnames(cnv_call) %in% colnames(norm_expr),drop=FALSE] - if (nrow(cnv_call)>0 & ncol(cnv_call)>0) - filter[rownames(cnv_call),colnames(cnv_call)] <- cnv_call - } - - tmp <- norm_expr - tmp[!filter] <- as.numeric(NA) - N <- rowSums(!is.na(tmp)) - m <- rowMeans(tmp, na.rm=TRUE) - s <- apply(tmp, 1, sd, na.rm=TRUE) - - s[s==0 | N 0) { - tmp[[i]] <- tmp[[i]][tmp[[i]]$Geneid %in% ids,,drop=FALSE] - if (nrow(tmp[[i]])<1 || any(is.na(tmp[[i]]$Geneid)) || any(duplicated(tmp[[i]]$Geneid))) - next - counts[tmp[[i]]$Geneid,i] <- tmp[[i]][,ncol(tmp[[i]])] - } - } - - counts -} - -#' Remap ids for gene expression count matrix -#' -#' Given a gene expression count matrix with ids stored as row names, the function maps these ids to ENTREZ ids, -#' and outputs a gene expression count matrix with ENTREZ ids as rownames. -#' -#' When several original ids map to the same ENTREZ id, the output value will be the median of each input entry. -#' -#' @param pip_counts Gene expression count matrix, with gene ids as row names -#' @param org_obj Bioconductor organism description object containing mappings between original & ENTREZ gene ids (default: human) -#' @param pipeline_id type of ids stored in the pip_counts row names ("ENSEMBL" by default) -#' @param FUNC which value to use in presence of multiple pipeline genes for one ENTREZ gene (default: max) -#' -#' @return gene expression count matrix for ENTREZ genes -#' @export -#' -#' @examples -pipeline_to_entrez <- function(pip_counts, org_obj=org.Hs.eg.db::org.Hs.eg.db, pipeline_id="ENSEMBL", FUNC=max) { - if (missing(pip_counts) || is.null(pip_counts) || - !is.matrix(pip_counts) || nrow(pip_counts)<1 || ncol(pip_counts)<1 || - !is.numeric(pip_counts) || - is.null(rownames(pip_counts)) || any(is.na(rownames(pip_counts))) || any(rownames(pip_counts)=="")) - stop("Missing/illegal counts matrix") - if (is.null(pipeline_id) || !is.character(pipeline_id) || length(pipeline_id)!=1 || is.na(pipeline_id) || - pipeline_id=="") - stop("Missing, illegal or unknown pipeline id type") - if (pipeline_id == "ENTREZID") return(pip_counts) - if (is.null(org_obj) || !is(org_obj, "OrgDb") || - !all(c(pipeline_id, "ENTREZID") %in% AnnotationDbi::columns(org_obj))) - stop("Missing/illegal organism database (OrgDb object)") - - ids <- AnnotationDbi::select(org_obj, - keys=rownames(pip_counts), - keytype=pipeline_id, - columns=c(pipeline_id, "ENTREZID")) - if (is.null(ids) || !is.data.frame(ids) || nrow(ids)<1) - stop("Pipeline ids not found") - ids <- ids[!is.na(ids[,pipeline_id]) & !is.na(ids[,"ENTREZID"]),] - if (nrow(ids)==0) - stop("No valid mappings") - ids[,pipeline_id] <- as.character(ids[,pipeline_id]) - ids[,"ENTREZID"] <- as.character(ids[,"ENTREZID"]) - - i <- split(ids[,pipeline_id], ids[,"ENTREZID"]) - i1 <- i[lengths(i)==1] - i2 <- i[lengths(i)>1] - - ent_counts <- c() - if (length(i1)>0) { - i1 <- unlist(i1) - tmp <- pip_counts[i1,] - rownames(tmp) <- names(i1) - ent_counts <- rbind(ent_counts, tmp) - } - if (length(i2)>0) { - tmp <- t(sapply(i2, function(j) apply(pip_counts[j,,drop=FALSE], 2, FUNC))) - ent_counts <- rbind(ent_counts, tmp) - } - - round(ent_counts) -} - -#' Normalise gene expression counts on regularised log scale -#' -#' @param counts gene expression count matrix (must be integer) -#' @param verbose DESeq2 normalisation progress messages -#' @param fast use vst instead of rlog to compute normalised expression -#' -#' @return matrix of normalised expression on regularised log scale -#' @export -#' -#' @examples -normalise_counts <- function(counts, verbose=FALSE, fast=FALSE) { - if (missing(counts) || is.null(counts) || - !is.matrix(counts) || nrow(counts)<1 || ncol(counts)<1 || - !is.numeric(counts) || any(is.na(counts)) || any(counts<0) || - is.null(rownames(counts)) || any(is.na(rownames(counts))) || any(rownames(counts)=="") || - is.null(colnames(counts)) || any(is.na(colnames(counts))) || any(colnames(counts)=="")) - stop("Missing/illegal counts matrix") - - donors <- data.frame(Donor=colnames(counts), stringsAsFactors=FALSE) - - normalised <- DESeq2::DESeqDataSetFromMatrix( - countData=counts, colData=donors, design=as.formula("~ 1"), tidy=FALSE - ) - normalised <- DESeq2::DESeq(normalised, betaPrior=TRUE, quiet=!verbose) - if (fast) { - normalised <- DESeq2::vst(normalised, blind=TRUE) - } else { - normalised <- DESeq2::rlog(normalised, blind=TRUE) - } - SummarizedExperiment::assay(normalised) -} - -#' Merge gene-based CNV results -#' -#' @param df gene calls file names -#' -#' @return data.frame with one row per gene and one column per donor. -#' The first two columns are Hugo_Symbol (HGNC gene name) & Entrez_Gene_Id. -#' Only genes with positive ENTREZ ids are returned. -#' @export -#' -#' @examples -process_cnv_genes <- function(df) { - if (missing(df) || is.null(df) || !is.data.frame(df) || nrow(df)==0) - stop("Missing or illegal CNV files data frame") - - df <- df %>% - dplyr::filter(!is.na(filename) & file.access(filename, mode=4)==0) - - unprocessed <- c() - rslt <- NULL - for (i in 1:nrow(df)) { - x <- read.table(df$filename[i], sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE) - x <- x[rowSums(is.na(x))==0,] - - # Workaround a bug in the first versions of the copywriter target_seq_cnv_calling step - if (colnames(x)[1] == "Hugo_Gene_Symbol") colnames(x)[1] <- "Hugo_Symbol" - - if (ncol(x) != 3 || !all(colnames(x)[1:2] == c("Hugo_Symbol", "Entrez_Gene_Id"))) { - unprocessed <- c(unprocessed, df$ID[i]) - next - } - - if (is.null(rslt)) { - rslt <- x[,1:2] - ref_hash <- paste(rslt$Hugo_Symbol, rslt$Entrez_Gene_Id, sep="\t") - } - - x_hash <- paste(x$Hugo_Symbol, x$Entrez_Gene_Id, sep="\t") - - rslt <- rslt[ref_hash %in% x_hash,] - ref_hash <- ref_hash[ref_hash %in% x_hash] - x <- x[match(ref_hash, x_hash),] - - rslt <- cbind(rslt, x[,3]) - colnames(rslt)[ncol(rslt)] <- df$ID[i] - } - - if (length(unprocessed) > 0) - warning("Gene CNA data could not be processed for donors ", paste(unprocessed, collapse=", ")) - - if (all(grepl("^ *[+-]?[0-9]+ *$", rslt$Entrez_Gene_Id))) { - rslt$Entrez_Gene_Id <- as.integer(rslt$Entrez_Gene_Id) - if ("Entrez_Gene_Id" %in% colnames(rslt)) - rslt <- rslt %>% dplyr::filter(Entrez_Gene_Id>0) - } else { - warning("Non-numerical Entrez_Gene_Id records") - } - - if (any(duplicated(rslt$Entrez_Gene_Id))) { - warning("Duplicated ENTREZ genes ", - paste(unique(rslt$Entrez_Gene_Id[duplicated(rslt$Entrez_Gene_Id)]), collapse=", ")) - rslt <- rslt[!duplicated(rslt$Entrez_Gene_Id),] - } - - rslt -} - diff --git a/snappy_wrappers/wrappers/cbioportal/study_meta/environment.yaml b/snappy_wrappers/wrappers/cbioportal/study_meta/environment.yaml deleted file mode 100644 index 40e802f1b..000000000 --- a/snappy_wrappers/wrappers/cbioportal/study_meta/environment.yaml +++ /dev/null @@ -1 +0,0 @@ -name: cbio_meta_study diff --git a/snappy_wrappers/wrappers/cbioportal/study_meta/wrapper.py b/snappy_wrappers/wrappers/cbioportal/study_meta/wrapper.py deleted file mode 100644 index 18cdae52a..000000000 --- a/snappy_wrappers/wrappers/cbioportal/study_meta/wrapper.py +++ /dev/null @@ -1,28 +0,0 @@ -# -*- coding: utf-8 -*- -"""cbioportal metadata helper functions""" - - -def create_study_meta_file(config, outfile): - """Write study meta file, given study metadata""" - s = "\n".join( - [ - "type_of_cancer: {type_of_cancer}", - "cancer_study_identifier: {cancer_study_id}", - "name: {study_name}", - "short_name: {study_name_short}", - "description: {study_description}", - "add_global_case_list: true", - ] - ).format( - type_of_cancer=config["step_config"]["cbioportal_export"]["type_of_cancer"], - cancer_study_id=config["step_config"]["cbioportal_export"]["cancer_study_id"], - study_description=config["step_config"]["cbioportal_export"]["study_description"], - study_name=config["step_config"]["cbioportal_export"]["study_name"], - study_name_short=config["step_config"]["cbioportal_export"]["study_name_short"], - ) - with open(outfile, "w") as out: - out.write(s) - out.write("\n") - - -create_study_meta_file(snakemake.config, snakemake.output.meta_file) diff --git a/snappy_wrappers/wrappers/cbioportal/zscores/environment.yaml b/snappy_wrappers/wrappers/cbioportal/zscores/environment.yaml deleted file mode 100644 index 8a1dc15af..000000000 --- a/snappy_wrappers/wrappers/cbioportal/zscores/environment.yaml +++ /dev/null @@ -1,11 +0,0 @@ -channels: -- bioconda -- conda-forge -- anaconda -dependencies: -- r >=3.6 -- r-dplyr -- bioconductor-DESeq2 >=1.26 -- bioconductor-org.hs.eg.db -- bioconductor-txdb.hsapiens.ucsc.hg19.knowngene -- openblas diff --git a/snappy_wrappers/wrappers/cbioportal/zscores/scripts.R b/snappy_wrappers/wrappers/cbioportal/zscores/scripts.R deleted file mode 120000 index 87d0b3815..000000000 --- a/snappy_wrappers/wrappers/cbioportal/zscores/scripts.R +++ /dev/null @@ -1 +0,0 @@ -../scripts.R \ No newline at end of file diff --git a/snappy_wrappers/wrappers/cbioportal/zscores/snappy-run-zscores.R b/snappy_wrappers/wrappers/cbioportal/zscores/snappy-run-zscores.R deleted file mode 100644 index 001e88508..000000000 --- a/snappy_wrappers/wrappers/cbioportal/zscores/snappy-run-zscores.R +++ /dev/null @@ -1,376 +0,0 @@ -#' Aggregates counts and creates z-scores file -#' -#' Pipeline-implementation agnostic, location of files defined in the input data.frame -#' -#' @param df data frame describing expression counts & CNV gene calls files -#' @param count_input_format gene expression counts file format (only "feature_counts" supported) -#' @param gene_call_input_format CNV gene calls file format (only "cubi_pipeline" supported) -#' @param org_obj Bioconductor organism object (human by default) -#' @param pipeline_id type of ids used by the pipeline ("ENSEMBL" by default) -#' @param symbol_id Hugo_Symbol id name in org_obj ("SYMBOL" by default) -#' @param min_nb_diploid minimum number of diploid samples in order to compute z-scores (default 10) -#' @param verbose show progress of the computation -#' @param fast use vst instead of rlog to compute normalised expression -#' -#' @return the z_score data frame -#' @export -#' -#' @examples -compute_z_scores <- function( - df, - count_input_format="feature_counts", - gene_call_input_format="cubi_pipeline", - org_obj=org.Hs.eg.db::org.Hs.eg.db, pipeline_id="ENSEMBL", symbol_id="SYMBOL", - min_nb_diploid=10, - verbose=FALSE, fast=FALSE -) { - if (missing(df) || is.null(df) || !is.data.frame(df) || nrow(df)<1 || - !all(c("ID", "count_filename", "gene_call_filename") %in% colnames(df))) - stop("Missing or illegal directory path") - if (any(is.na(df$ID) | df$ID=="") || any(duplicated(df$ID))) - stop("Illegal ID column") - if (is.null(count_input_format) || - !is.character(count_input_format) || length(count_input_format)!=1 || is.na(count_input_format)) - stop("Missing or illegal file format for gene expression counts") - count_input_format <- match.arg(count_input_format) - if (is.null(gene_call_input_format) || !is.character(gene_call_input_format) || length(gene_call_input_format)!=1 || is.na(gene_call_input_format)) - stop("Missing or illegal file format for CNV gene calls") - gene_call_input_format <- match.arg(gene_call_input_format) - if (is.null(org_obj) || !is(org_obj, "OrgDb")) - stop("Missing or illegal organism description object") - if (is.null(pipeline_id) || !is.character(pipeline_id) || length(pipeline_id)!=1 || is.na(pipeline_id) || - pipeline_id=="" || !(pipeline_id %in% AnnotationDbi::columns(org_obj))) - stop("Missing, illegal or unknown pipeline id type") - if (is.null(symbol_id) || !is.character(symbol_id) || length(symbol_id)!=1 || is.na(symbol_id) || - symbol_id=="" || !(symbol_id %in% AnnotationDbi::columns(org_obj))) - stop("Missing, illegal or unknown Hugo_Symbol id type") - - # Identify samples with expression files - has_expr <- !is.na(df$count_filename) & df$count_filename!="" & file.access(df$count_filename, mode=4)==0 - names(has_expr) <- as.character(df$ID) - if (!any(has_expr)) - stop("No valid gene expression count file") - - # Read counts counts - if (verbose) cat("Read expression counts ... ") - counts <- switch( - count_input_format, - feature_counts=read_featurecounts_files(df$count_filename[has_expr]) - ) - colnames(counts) <- df$ID[has_expr] - rownames(counts) <- sub("\\.[0-9]+$", "", rownames(counts)) - if (verbose) cat("Done\n") - - # Remove samples with no expression counts (all NA) - has_expr[colnames(counts)] <- has_expr[colnames(counts)] & (colSums(!is.na(counts))>0) - if (!any(has_expr)) - stop("No gene expression sample with valid expression counts") - counts <- counts[,colSums(!is.na(counts))>0,drop=FALSE] - - # Remap counts to ENTREZ gene ids - if (verbose) cat("Convert gene ids from ENSEMBL to ENTREZ ... ") - counts <- pipeline_to_entrez(counts, org_obj=org_obj, pipeline_id=pipeline_id) - if (verbose) cat("Done\n") - - # Normalise counts - if (verbose) cat("Normalise expression ... ") - has_expr[colnames(counts)] <- has_expr[colnames(counts)] & (colSums(is.na(counts))==0) - counts <- counts[,colSums(is.na(counts))==0,drop=FALSE] # Required for DESeq2::DESeq - if (!any(has_expr)) - stop("No valid gene expression sample for normalisation") - expr <- normalise_counts(counts, verbose=verbose, fast=fast) - if (verbose) cat("Done\n") - - # Identify files with CNV gene calls and - has_cnv <- !is.na(df$gene_call_filename) & df$gene_call_filename!="" & file.access(df$gene_call_filename, mode=0)==0 - has_both <- has_expr & has_cnv - - cnv_calls <- NULL - if (any(has_both)) { - if (verbose) cat("Read CNV gene calls ... ") - cnv_calls <- switch( - gene_call_input_format, - cubi_pipeline=process_cnv_genes(df[has_both,] %>% dplyr::rename(filename=gene_call_filename)) - ) - - rownames(cnv_calls) <- as.character(cnv_calls$Entrez_Gene_Id) - cnv_calls <- cnv_calls %>% dplyr::select(-Hugo_Symbol, -Entrez_Gene_Id) %>% as.matrix() - colnames(cnv_calls) <- df$ID[has_both] - if (verbose) cat("Done\n") - } - - # Compute z-scores (when no CNV calls are present, use all samples) - if (verbose) cat("Compute expression z-scores ... ") - z <- z_scores(expr, cnv_calls, min_nb_diploid=min_nb_diploid) - if (verbose) cat("Done\n") - - # Gene symbols from ENTREZ ids - if (verbose) cat("Add gene symbols ... ") - if (any(has_both)) { - gene_names <- process_cnv_genes(df[has_both,] %>% dplyr::rename(filename=gene_call_filename)) %>% - dplyr::select(Hugo_Symbol, Entrez_Gene_Id) - } else { - if (!all(c(symbol_id, "ENTREZID") %in% AnnotationDbi::columns(org_obj))) - stop("Missing/illegal organism database (OrgDb object)") - - gene_names <- AnnotationDbi::select( - org_obj, - keys=rownames(z), - keytype="ENTREZID", - columns=c(symbol_id, "ENTREZID") - ) - if (is.null(gene_names) || !is.data.frame(gene_names) || nrow(gene_names)<1) - stop("Entrez_Gene_Id ids not found") - gene_names <- gene_names[!is.na(gene_names$SYMBOL) & !is.na(gene_names$ENTREZID),] - if (nrow(gene_names)==0) - stop("No valid mappings") - colnames(gene_names) <- c("Hugo_Symbol", "Entrez_Gene_Id") - } - if (verbose) cat("Done\n") - - # Make data frame with Hugo_Symbol, Entrez_Gene_Id and z-scores columns - z <- z[rownames(z) %in% as.character(gene_names$Entrez_Gene_Id),,drop=FALSE] - i <- match(rownames(z), as.character(gene_names$Entrez_Gene_Id)) - z <- data.frame(gene_names[i,], z, stringsAsFactors=FALSE, check.names=FALSE) - rownames(z) <- NULL - - z -} - - -#' Read feature_count output files -#' -#' @param fns feature counts output file names -#' -#' @return a numeric matrix of counts, with gene ids as row names -#' @export -#' -#' @examples -read_featurecounts_files <- function(fns) { - if (missing(fns) || !is.character(fns) || length(fns)==0 || sum(!is.na(fns) & fns!="")==0) - stop("Missing/illegal featurecounts file names") - - tmp <- lapply(fns, function(x) { - if (is.na(x) || x=="" || !file.exists(x) || file.access(x, mode=4)!=0) - return(data.frame(Geneid=as.character(), Counts=as.integer(), stringsAsFactors=FALSE)) - read.table(x, sep="\t", header=1, stringsAsFactors=FALSE) - }) - - ids <- unique(unlist(lapply(tmp, function(x) x$Geneid))) - ids <- ids[!is.na(ids)] - if( length(ids) == 0) - stop("No readable non-empty featurecounts file") - - counts <- matrix(as.numeric(NA), nrow=length(ids), ncol=length(tmp), dimnames=list(ids, fns)) - for (i in 1:length(tmp)) { - if (nrow(tmp[[i]]) > 0) - counts[tmp[[i]]$Geneid,i] <- tmp[[i]][,ncol(tmp[[i]])] - } - - counts -} - - -#' Remap ids for gene expression count matrix -#' -#' Given a gene expression count matrix with ids stored as row names, the function maps these ids to ENTREZ ids, -#' and outputs a gene expression count matrix with ENTREZ ids as rownames. -#' -#' When several original ids map to the same ENTREZ id, the output value will be the median of each input entry. -#' -#' @param pip_counts Gene expression count matrix, with gene ids as row names -#' @param org_obj Bioconductor organism description object containing mappings between original & ENTREZ gene ids (default: human) -#' @param pipeline_id type of ids stored in the pip_counts row names ("ENSEMBL" by default) -#' -#' @return gene expression count matrix for ENTREZ genes -#' @export -#' -#' @examples -pipeline_to_entrez <- function(pip_counts, org_obj=org.Hs.eg.db::org.Hs.eg.db, pipeline_id="ENSEMBL") { - if (missing(pip_counts) || is.null(pip_counts) || !is.matrix(pip_counts) || nrow(pip_counts)<1 || ncol(pip_counts)<1 || - !is.numeric(pip_counts) || is.null(rownames(pip_counts)) || any(is.na(rownames(pip_counts))) || any(rownames(pip_counts)=="")) - stop("Missing/illegal counts matrix") - if (is.null(pipeline_id) || !is.character(pipeline_id) || length(pipeline_id)!=1 || is.na(pipeline_id) || pipeline_id=="") - stop("Missing, illegal or unknown pipeline id type") - if (pipeline_id == "ENTREZID") return(pip_counts) - if (is.null(org_obj) || !is(org_obj, "OrgDb") || !all(c(pipeline_id, "ENTREZID") %in% AnnotationDbi::columns(org_obj))) - stop("Missing/illegal organism database (OrgDb object)") - - ids <- AnnotationDbi::select( - org_obj, - keys=rownames(pip_counts), - keytype=pipeline_id, - columns=c(pipeline_id, "ENTREZID") - ) - if (is.null(ids) || !is.data.frame(ids) || nrow(ids)<1) - stop("Pipeline ids not found") - ids <- ids[!is.na(ids[,pipeline_id]) & !is.na(ids[,"ENTREZID"]),] - if (nrow(ids)==0) - stop("No valid mappings") - ids[,pipeline_id] <- as.character(ids[,pipeline_id]) - ids[,"ENTREZID"] <- as.character(ids[,"ENTREZID"]) - - i <- split(ids[,pipeline_id], ids[,"ENTREZID"]) - i1 <- i[lengths(i)==1] - i2 <- i[lengths(i)>1] - - ent_counts <- c() - if (length(i1)>0) { - i1 <- unlist(i1) - tmp <- pip_counts[i1,,drop=FALSE] - rownames(tmp) <- names(i1) - ent_counts <- rbind(ent_counts, tmp) - } - if (length(i2)>0) { - tmp <- sapply(i2, function(j) apply(pip_counts[j,,drop=FALSE], 2, median)) - tmp <- t(matrix(as.vector(tmp), nrow=ncol(pip_counts), ncol=length(i2), dimnames=list(colnames(pip_counts), names(i2)))) - ent_counts <- rbind(ent_counts, tmp) - } - - round(ent_counts) -} - - -#' Normalise gene expression counts on regularised log scale -#' -#' @param counts gene expression count matrix (must be integer) -#' @param verbose DESeq2 normalisation progress messages -#' @param fast use vst instead of rlog to compute normalised expression -#' -#' @return matrix of normalised expression on regularised log scale -#' @export -#' -#' @examples -normalise_counts <- function(counts, verbose=FALSE, fast=FALSE) { - if (missing(counts) || is.null(counts) || !is.matrix(counts) || nrow(counts)<1 || ncol(counts)<1 || - !is.numeric(counts) || any(is.na(counts)) || any(counts<0) || - is.null(rownames(counts)) || any(is.na(rownames(counts))) || any(rownames(counts)=="") || - is.null(colnames(counts)) || any(is.na(colnames(counts))) || any(colnames(counts)=="")) - stop("Missing/illegal counts matrix") - - donors <- data.frame(Donor=colnames(counts), stringsAsFactors=FALSE) - - normalised <- DESeq2::DESeqDataSetFromMatrix( - countData=counts, colData=donors, design=as.formula("~ 1"), tidy=FALSE - ) - normalised <- DESeq2::DESeq(normalised, betaPrior=TRUE, quiet=!verbose) - if (fast) { - normalised <- DESeq2::vst(normalised, blind=TRUE) - } else { - normalised <- DESeq2::rlog(normalised, blind=TRUE) - } - SummarizedExperiment::assay(normalised) -} - - - -#' Merge gene-based CNV results -#' -#' @param df gene calls file names -#' -#' @return data.frame with one row per gene and one column per donor. -#' The first two columns are Hugo_Symbol (HGNC gene name) & Entrez_Gene_Id. -#' Only genes with positive ENTREZ ids are returned. -#' @export -#' -#' @examples -process_cnv_genes <- function(df) { - if (missing(df) || is.null(df) || !is.data.frame(df) || nrow(df)==0) - stop("Missing or illegal CNV files data frame") - - df <- df %>% - dplyr::filter(!is.na(filename) & file.access(filename, mode=4)==0) - - unprocessed <- c() - rslt <- NULL - for (i in 1:nrow(df)) { - x <- read.table(df$filename[i], sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE) - x <- x[rowSums(is.na(x))==0,] - - # Workaround a bug in the first versions of the copywriter target_seq_cnv_calling step - if (colnames(x)[1] == "Hugo_Gene_Symbol") colnames(x)[1] <- "Hugo_Symbol" - - if (ncol(x) != 3 || !all(colnames(x)[1:2] == c("Hugo_Symbol", "Entrez_Gene_Id"))) { - unprocessed <- c(unprocessed, df$ID[i]) - next - } - - if (is.null(rslt)) { - rslt <- x[,1:2] - ref_hash <- paste(rslt$Hugo_Symbol, rslt$Entrez_Gene_Id, sep="\t") - } - - x_hash <- paste(x$Hugo_Symbol, x$Entrez_Gene_Id, sep="\t") - - rslt <- rslt[ref_hash %in% x_hash,] - ref_hash <- ref_hash[ref_hash %in% x_hash] - x <- x[match(ref_hash, x_hash),] - - rslt <- cbind(rslt, x[,3]) - colnames(rslt)[ncol(rslt)] <- df$ID[i] - } - - if (length(unprocessed) > 0) - warning("Gene CNA data could not be processed for donors ", paste(unprocessed, collapse=", ")) - - if (all(grepl("^ *[+-]?[0-9]+ *$", rslt$Entrez_Gene_Id))) { - rslt$Entrez_Gene_Id <- as.integer(rslt$Entrez_Gene_Id) - if ("Entrez_Gene_Id" %in% colnames(rslt)) - rslt <- rslt %>% dplyr::filter(Entrez_Gene_Id>0) - } else { - warning("Non-numerical Entrez_Gene_Id records") - } - - if (any(duplicated(rslt$Entrez_Gene_Id))) { - warning("Duplicated ENTREZ genes ", paste(unique(rslt$Entrez_Gene_Id[duplicated(rslt$Entrez_Gene_Id)]), collapse=", ")) - rslt <- rslt[!duplicated(rslt$Entrez_Gene_Id),] - } - - rslt -} - - - -#' Compute gene expression z-scores from diploid samples -#' -#' @param norm_expr normalised expression matrix -#' @param cnv_calls matrix of calls (0 for diploid) -#' @param min_nb_diploid minimum number of diploid samples in order to compute z-scores (default 10) -#' -#' @return a matrix of z scores -#' @export -#' -#' @examples -z_scores <- function(norm_expr, cnv_call=NULL, min_nb_diploid=10) { - if (missing(norm_expr) || is.null(norm_expr) || !is.matrix(norm_expr) || nrow(norm_expr)<1 || ncol(norm_expr)<1 || - !is.numeric(norm_expr) || any(is.na(norm_expr)) || - is.null(rownames(norm_expr)) || any(is.na(rownames(norm_expr))) || any(rownames(norm_expr)=="") || - is.null(colnames(norm_expr)) || any(is.na(colnames(norm_expr))) || any(colnames(norm_expr)=="")) - stop("Missing/illegal normalised expression matrix") - if (is.null(min_nb_diploid) || !is.numeric(min_nb_diploid) || length(min_nb_diploid)!=1 || is.na(min_nb_diploid) || min_nb_diploid<0) - stop("Missing/illegal minimum number of diploid samples") - if (min_nb_diploid<3) min_nb_diploid <- 3 - - filter <- matrix(TRUE, nrow=nrow(norm_expr), ncol=ncol(norm_expr), dimnames=dimnames(norm_expr)) - - if (!is.null(cnv_call)) { - if (!is.matrix(cnv_call) || nrow(cnv_call)<1 || ncol(cnv_call)<1 || - is.null(rownames(cnv_call)) || any(is.na(rownames(cnv_call))) || any(rownames(cnv_call)=="") || - is.null(colnames(cnv_call)) || any(is.na(colnames(cnv_call))) || any(colnames(cnv_call)=="")) - stop("Illegal gene-based copy-number matrix") - cnv_call <- !is.na(cnv_call) & cnv_call==0 - cnv_call <- cnv_call[rownames(cnv_call) %in% rownames(norm_expr),colnames(cnv_call) %in% colnames(norm_expr),drop=FALSE] - if (nrow(cnv_call)>0 & ncol(cnv_call)>0) - filter[rownames(cnv_call),colnames(cnv_call)] <- cnv_call - } - - tmp <- norm_expr - tmp[!filter] <- as.numeric(NA) - N <- rowSums(!is.na(tmp)) - m <- rowMeans(tmp, na.rm=TRUE) - s <- apply(tmp, 1, sd, na.rm=TRUE) - - s[s==0 | N >(tee -a "{snakemake.log}" >&2) - else - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - echo "No tty, logging disabled" >"{snakemake.log}" - fi -fi - -# ------------------------------------------------------------------------------------------------- -# Write helper script and call R -# -cat <<"EOF" > $TMPDIR/compute_zscores.R -library( magrittr ) -library( methods ) # https://github.com/tidyverse/broom/issues/67 -source( "{rscript}" ) - -zscores_mapping_df <- read.table("{snakemake.input.tsv}", sep="\t", head=1, stringsAsFactors=FALSE) - -zscores = compute_z_scores(df = zscores_mapping_df, min_nb_diploid=5) - -mapping_df <- read.table("{snakemake.input.tsv}", sep="\t", header=1, stringsAsFactors=FALSE) -zscores = compute_z_scores(df = mapping_df, min_nb_diploid=5) -write.table(zscores, file="{snakemake.output.tsv}", sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE) - -warnings() -sessionInfo() -EOF - -Rscript --vanilla $TMPDIR/compute_zscores.R -""" -) diff --git a/snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml b/snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml new file mode 100644 index 000000000..e936461b1 --- /dev/null +++ b/snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml @@ -0,0 +1,7 @@ +channels: +- conda-forge +- bioconda +- r +dependencies: +- r-base +- bioconductor-genomicranges diff --git a/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py b/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py new file mode 100644 index 000000000..f79a46585 --- /dev/null +++ b/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py @@ -0,0 +1,82 @@ +# -*- coding: utf-8 -*- +"""Wrapper vor cnvkit.py call +""" + +from snakemake.shell import shell + +__author__ = "Manuel Holtgrewe" +__email__ = "manuel.holtgrewe@bih-charite.de" + +shell( + r""" +# Also pipe everything to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec &> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +set -x + +# ----------------------------------------------------------------------------- + +cat << _EOF | R --vanilla --slave +segments <- read.table("{snakemake.input.segment}", sep="\t", header=1, stringsAsFactors=FALSE) +stopifnot(all(c("chromosome", "start", "end") %in% colnames(segments))) +calls <- read.table("{snakemake.input.call}", sep="\t", header=1, stringsAsFactors=FALSE) +stopifnot(all(c("chromosome", "start", "end", "cn") %in% colnames(calls))) + +# Trim segments to avoid edge effects with calls +segments[,"start"] <- segments[["start"]]+1 +segments[,"end"] <- segments[["end"]]-1 +segments <- segments[segments[["end"]]-segments[["start"]]>0,] + +r1 <- GenomicRanges::GRanges( + seqnames=segments[["chromosome"]], + ranges=IRanges::IRanges(start=segments[["start"]], end=segments[["end"]]), + strand="*" +) +r2 <- GenomicRanges::GRanges( + seqnames=calls[["chromosome"]], + ranges=IRanges::IRanges(start=calls[["start"]], end=calls[["end"]]), + strand="*" +) + +i <- GenomicRanges::findOverlaps(r1, r2, ignore.strand=TRUE) +stopifnot(!any(duplicated(S4Vectors::queryHits(i)))) + +# Default value: diploid segment (number of copies = 2) +segments[,"cn"] <- 2 +segments[S4Vectors::queryHits(i),"cn"] <- calls[S4Vectors::subjectHits(i),"cn"] + +# Reset segment boundaries to original values +segments[,"start"] <- segments[["start"]]-1 +segments[,"end"] <- segments[["end"]]+1 + +write.table(segments, file="{snakemake.output.final}", sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE) +_EOF + +d=$(dirname "{snakemake.output.final}") +pushd $d +fn=$(basename "{snakemake.output.final}") +md5sum $fn > $fn.md5 +popd +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/rseqc/wrapper.py b/snappy_wrappers/wrappers/rseqc/wrapper.py index f8f1b2067..93730e6b8 100644 --- a/snappy_wrappers/wrappers/rseqc/wrapper.py +++ b/snappy_wrappers/wrappers/rseqc/wrapper.py @@ -1,13 +1,22 @@ # -*- coding: utf-8 -*- -"""CUBI+Snakemake wrapper code for FeatureCounts: Snakemake wrapper.py +"""CUBI+Snakemake wrapper code for infer_experiment: Snakemake wrapper.py """ +import os + from snakemake import shell __author__ = "Clemens Messerschmidt " shell.executable("/bin/bash") +current_step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][current_step]["strandedness"] +out_link_dir = ( + os.path.dirname(snakemake.output.output) if "output" in snakemake.output.keys() else "" +) +log_link_dir = os.path.dirname(snakemake.output.log) if "log" in snakemake.output.keys() else "" + shell( r""" set -euo pipefail @@ -17,63 +26,114 @@ export TMPDIR=$(mktemp -d) trap "rm -rf $TMPDIR" EXIT +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + + # Also pipe stderr to log file -if [[ -n "{snakemake.log}" ]]; then +if [[ -n "{snakemake.log.log}" ]]; then if [[ "$(set +e; tty; set -e)" != "" ]]; then - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - exec 2> >(tee -a "{snakemake.log}" >&2) + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) else - rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log}) - echo "No tty, logging disabled" >"{snakemake.log}" + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" fi fi -# Run rseqc to infer strandedness +# ----- Run rseqc to infer strandedness infer_experiment.py \ - -r "{snakemake.config[step_config][gene_expression_quantification][strandedness][path_exon_bed]}" \ + -r "{config[path_exon_bed]}" \ -i "{snakemake.input.bam}" \ > "{snakemake.output.tsv}" -md5sum {snakemake.output.tsv} > {snakemake.output.tsv_md5} +# ----- Parse rseqc infer_experiment output +pattern="^This is (Pair|Single)End Data$" +endedness=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") + +pattern="^Fraction of reads failed to determine: *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" +failed=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") -# Set strandedness based on input parameter or inferred value -strand={snakemake.config[step_config][gene_expression_quantification][strand]} -if [ ${{strand}} -eq -1 ] +if [[ "$endedness" = "Single" ]] then - pattern="^This is (Pair|Single)End Data$" - endedness=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") - - pattern="^Fraction of reads failed to determine: *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" - failed=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") - - if [ "$endedness" == "Single" ] - then - pattern="^Fraction of reads explained by \"\\+\\+,\\-\\-\": *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" - forward=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") - pattern="^Fraction of reads explained by \"\\+\\-,\\-\\+\": *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" - reverse=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") - else - pattern="^Fraction of reads explained by \"1\\+\\+,1\\-\\-,2\\+\\-,2\\-\\+\": *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" - forward=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") - pattern="^Fraction of reads explained by \"1\\+\\-,1\\-\\+,2\\+\\+,2\\-\\-\": *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" - reverse=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") - fi + pattern="^Fraction of reads explained by \"\\+\\+,\\-\\-\": *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" + forward=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") + pattern="^Fraction of reads explained by \"\\+\\-,\\-\\+\": *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" + reverse=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") +else + pattern="^Fraction of reads explained by \"1\\+\\+,1\\-\\-,2\\+\\-,2\\-\\+\": *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" + forward=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") + pattern="^Fraction of reads explained by \"1\\+\\-,1\\-\\+,2\\+\\+,2\\-\\-\": *([+-]?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([EeDd][+-]?[0-9]+)?)$" + reverse=$(grep -E "$pattern" {snakemake.output.tsv} | sed -E "s/$pattern/\1/") +fi - reverse=$(echo $reverse | tr '[Dde]' 'E') +forward=$(echo $forward | tr '[Dde]' 'E') +reverse=$(echo $reverse | tr '[Dde]' 'E') - strand=0 - if [ $(echo "$forward > {snakemake.config[step_config][gene_expression_quantification][strandedness][threshold]}" | bc -l) -gt 0 ] - then - strand=1 - fi - if [ $(echo "$reverse > {snakemake.config[step_config][gene_expression_quantification][strandedness][threshold]}" | bc -l) -gt 0 ] - then - strand=2 - fi +# ----- Infer protocol strandedness +infer=0 +if [ $(echo "$forward > {config[threshold]}" | bc -l) -gt 0 ] +then + infer=1 +fi +if [ $(echo "$reverse > {config[threshold]}" | bc -l) -gt 0 ] +then + infer=2 fi -# Write strandedness -echo ${{strand}} > {snakemake.output.decision} -md5sum {snakemake.output.decision} > {snakemake.output.decision_md5} +decision="{config[strand]}" +if [[ $decision -eq -1 ]] +then + decision=$infer +fi + +# ----- Write outputs +md5=$(cat {config[path_exon_bed]} | md5sum | sed -e "s/ .*//") +cat << __EOF > {snakemake.output.decision} +{{ + "library_name": "{snakemake.wildcards[library_name]}", + "bed_path": "{config[path_exon_bed]}", + "bed_file_md5": "$md5", + "bam_path": "{snakemake.input.bam}", + "strand_from_user": "{config[strand]}, + "strand_from_infer": "$decision", + "decision_threshold": {config[threshold]}, + "endedness": "$endedness", + "fraction_forward": $forward, + "fraction_reverse": $reverse, + "fraction_failed": $failed, + "decision": "$decision" +}} +__EOF + +pushd $(dirname {snakemake.output.decision}) +md5sum $(basename {snakemake.output.decision}) > $(basename {snakemake.output.decision}).md5 +md5sum $(basename {snakemake.output.tsv}) > $(basename {snakemake.output.tsv}).md5 +popd + +if [[ -n "{out_link_dir}" ]]; +then + ln -sr {snakemake.output.decision} {out_link_dir}/. + ln -sr {snakemake.output.decision}.md5 {out_link_dir}/. +fi +if [[ -n "{log_link_dir}" ]]; +then + ln -sr {snakemake.log.log} {log_link_dir}/. + ln -sr {snakemake.log.log}.md5 {log_link_dir}/. + ln -sr {snakemake.log.conda_list} {log_link_dir}/. + ln -sr {snakemake.log.conda_list}.md5 {log_link_dir}/. + ln -sr {snakemake.log.conda_info} {log_link_dir}/. + ln -sr {snakemake.log.conda_info}.md5 {log_link_dir}/. +fi +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} """ ) diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/action.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/action.py new file mode 100644 index 000000000..8980f01a8 --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/action.py @@ -0,0 +1,10 @@ +from enum import Enum + + +class Action(Enum): + ERROR = 0 + STOP = 1 + SKIP = 2 + IGNORE = 3 + DEFAULT = 4 + OK = 5 diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/annotation.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/annotation.py new file mode 100644 index 000000000..d89af88bc --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/annotation.py @@ -0,0 +1,166 @@ +import re +import typing + +import exceptions +import vcfpy + + +class Annotation: + """Process jannovar ANN or vep CSQ INFO entries + + The configuration file must contain the INFO identifier (typically ANN or CSQ), and + regular expression to extract of column headers, and to split the annotation items. + For example, the configuration for annotations created by jannovar would be: + annotations: + id: "ANN" + extract: "^Functional annotations:'(.+)'$" + split: "\\|" + + The vcf header must be first parsed, to extract the column headers of the various + annotated fields. Then, the values of the records can be obtained. + + When there are multiple alternative alleles, annotations might be specific to a + particular one. In that case, there must be one column specifying the alternative + allele in the annotation. This information can be provided in the configuration by: + annotations: + id: "CSQ" + allele: "Allele" + """ + + def __init__( + self, + annotation_id: str, + extract: str, + split: str, + allele_column: str = None, + minimize: bool = False, + ): + """Create annotation object + + :param annotation_id: annotation ID in the vcf INFO fields + :param extract: regular expression string to extract column headers from the Description field + :param split: regular expression string to split the extracted contents of the Description field into column headers + :param allele_column: annotation column header to extract the alt allele (or None, when this information isn't present) + :param minimize: minimization of variants to patch a VEP bug + """ + if annotation_id is None or annotation_id == "": + raise exceptions.MissingValue("Missing annotation ID") + if not extract or not split: + raise exceptions.MissingValue( + 'Missing patterns for extraction "{}" or for split "{}"'.format(extract, split) + ) + self.annotation_id = annotation_id + self.allele_column = allele_column + self.columns = [] + self.extract = re.compile(extract) + self.split = re.compile(split) + self.minimize = minimize + self.minimizer = None + + def parseHeader(self, header: vcfpy.Header): + """Parse vcf header to extract annotation column headers + + :param header: vcf header as vcfpy.Header object + """ + ann_header = header.get_info_field_info(self.annotation_id) + if not ann_header: + raise exceptions.MissingValue( + 'Annotation "{}" cannot be found in vcf INFO fields'.format(self.annotation_id) + ) + m = self.extract.match(ann_header.description) + if m: + self.columns = self.split.split(m.group(1)) + else: + raise exceptions.IllegalValue( + 'Column headers can\'t be extracted from description "{}" by pattern "{}"'.format( + ann_header.description, self.extract + ) + ) + if self.allele_column: + if self.allele_column not in self.columns: + raise exceptions.MissingValue( + 'Allele column "{}" not in annotation "{}" columns {}'.format( + self.allele_column, self.annotation_id, self.columns + ) + ) + + def set_minimizer(self, record: vcfpy.Record): + """Create a minimizer object for alternate alleles + + ENSEMBL VEP annotates vcf records with minimized alternative allele sequence, + even without [`--minimal` option](https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html). + This undocumented feature is discussed in a [closed issue on github](https://github.com/Ensembl/ensembl-vep/issues/1264) + + To ensure that all variants are correctly processed, a minimizer must be created, + to match the sequences of the input and minimised variants. + This minimizer must be created for each record. + + :param record: vcf record + """ + minimisation = record.REF + for alt in record.ALT: + a = alt.value + i = 0 + while i < len(minimisation) and i < len(a) and minimisation[i] == a[i]: + i += 1 + if i < len(minimisation): + if i == 0: + minimisation = None + break + else: + minimisation = minimisation[:i] + if minimisation: + self.minimizer = {} + n = len(minimisation) + for alt in record.ALT: + if len(alt.value) == n: + self.minimizer["-"] = alt.value + else: + self.minimizer[alt.value[n:]] = alt.value + else: + self.minimizer = None + + def getAnnotations(self, record: vcfpy.Record) -> typing.Dict[str, typing.List[typing.Any]]: + """Extract annotations from a vcf record + + Depending on the choice of annotation software, there can be multiple annotations for a single variant. + The annotations may also depend on the alternative allele (when more than one are present). + The annotations are returned as a dict with the alternative alleles are keys. + If the annotations are allele-dependent, they are attributed to the allele, otherwise + all annotations are made available to all alleles. + For each allele, the annotations are given as a dict, with the column name as key, + and the list of annotations for that column as value. + + :param record: vcf record as vcfpy.Record object + :return: dict of of dict of annotation lists + """ + if record is None: + raise exceptions.MissingValue("Missing vcf record") + ann = record.INFO[self.annotation_id] + if not isinstance(ann, list): + ann = [ann] + alts = [alt.value for alt in record.ALT] + values = {} + for theColumn in self.columns: + values[theColumn] = {alt: None for alt in alts} + for a in ann: + one_ann = self._get_one_annotation(a) + storeAlts = self.columns + if self.allele_column and one_ann[self.allele_column] in alts: + storeAlts = [one_ann[self.allele_column]] + for k, v in one_ann.items(): + for alt in storeAlts: + if values[k][alt] is None: + values[k][alt] = [] + values[k][alt].append(v) + + return values + + def _get_one_annotation(self, annotation: str) -> typing.Dict[str, str]: + values = self.split.split(annotation) + assert len(values) == len(self.columns) + values = [x if x else None for x in values] + result = dict(zip(self.columns, values)) + if self.allele_column and self.minimizer and result[self.allele_column] in self.minimizer: + result[self.allele_column] = self.minimizer[result[self.allele_column]] + return result diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/common_functions.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/common_functions.py new file mode 100644 index 000000000..6429233be --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/common_functions.py @@ -0,0 +1,119 @@ +import re + + +def minimize_mutation(x, args): + assert isinstance(x, list) and len(x) == 3 + assert isinstance(x[0], list) and len(x[0]) == 1 + assert isinstance(x[1], list) and len(x[1]) == 1 + assert isinstance(x[2], list) and len(x[2]) == 1 + pos = int(x[0][0]) + ref = x[1][0] + alt = x[2][0] + + assert args is not None and isinstance(args, dict) and "return_value" in args.keys() + + # print("DEBUG- on input: pos = {}, ref = {}, alt = {}".format(pos, ref, alt)) + + i = 0 + # Trim common left part + while i < len(ref) and i < len(alt): + if ref[i] != alt[i]: + break + pos += 1 + i += 1 + if i == len(ref) and i == len(alt): + raise Exception("Reference and alternate sequences are identical") + ref = ref[i:] + alt = alt[i:] + + # print("DEBUG- on after left trim: pos = {}, ref = {}, alt = {}".format(pos, ref, alt)) + + # Trim common right part + i = 0 + while i < len(ref) and i < len(alt): + if ref[-i - 1] != alt[-i - 1]: + if i > 0: + ref = ref[:-i] + alt = alt[:-i] + break + i += 1 + + end = pos + len(ref) - 1 + + # print("DEBUG- on output: pos = {}, ref = {}, alt = {}".format(pos, ref, alt)) + + if ref == "": + ref = "-" + end = pos + pos -= 1 + if alt == "": + alt = "-" + + return_value = args["return_value"] + if return_value == "pos": + return [pos] + elif return_value == "ref": + return [ref] + elif return_value == "alt": + return [alt] + elif return_value == "end": + return [end] + else: + raise Exception('Unexpected return value request "{}"'.format(return_value)) + + +def calc_end_pos(x, args): + assert isinstance(x, list) and len(x) == 3 + assert isinstance(x[0], list) and len(x[0]) == 1 + assert isinstance(x[1], list) and len(x[1]) == 1 + assert isinstance(x[2], list) and len(x[2]) == 1 + pos = int(x[0][0]) + ref = x[1][0] + alt = x[2][0] + d = len(alt) - len(ref) + if d <= 0: + end = pos + len(ref) - 1 + else: + end = pos + 1 + return [end] + + +def variant_type(x, args=None): + assert isinstance(x, list) and len(x) == 2 + assert isinstance(x[0], list) and len(x[0]) == 1 + assert isinstance(x[1], list) and len(x[1]) == 1 + ref = x[0][0].replace("-", "") + alt = x[1][0].replace("-", "") + if len(ref) < len(alt): + variant_type = "INS" + elif len(ref) > len(alt): + variant_type = "DEL" + elif len(ref) == 0: + raise Exception("Empty reference & alternative allele sequences") + elif len(ref) == 1: + variant_type = "SNP" + elif len(ref) == 2: + variant_type = "DNP" + elif len(ref) == 3: + variant_type = "TNP" + else: + variant_type = "ONP" + return [variant_type] + + +strip_sequence_version_pattern = re.compile("\.[0-9]+$") # noqa: W605 + + +def strip_sequence_version(x, args): + if x is None: + return None + assert isinstance(x, list) and len(x) == 1 + if x[0] is None: + return None + no_version = list() + for el in x[0]: + if el is None: + no_version.append(None) + else: + no_version.append(strip_sequence_version_pattern.sub("", el)) + return no_version diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/config.yaml b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/config.yaml new file mode 100644 index 000000000..f442a1e04 --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/config.yaml @@ -0,0 +1,781 @@ +annotation: # Definition of annotations from VEP + id: "CSQ" # INFO field ID (unless change with --vcf_info_field option) + allele: "Allele" # Variant used to calculate consequence (https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#defaultout) + extract: "^Consequence annotations from Ensembl VEP. Format: (.+)$" # Regular expression to extract annotation names from the description of INFO field. The annotation names are in group 1 + split: "\\|" # Regular expression to split annotations (& annotation names) from the INFO field + minimize: True # Variant minimization applied by VEP (see https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#colocated) + + +output: # Output columns definition + + Hugo_Symbol: # Column name to output HGNC Symbol + input: # Required input + - set: "annotation" # The "SYMBOL" annotation column contains the requested information + column: "SYMBOL" + on_missing: skip # Genomic regions variants are not attached to genes, skip them on output + + Entrez_Gene_Id: # Column name to output NCBI ID + input: + - set: "annotation" # VEP doesn't provide NCBI gene ids (formerly ENTREZ gene ids) + column: "SYMBOL" # The column value is obtained by mapping the HGNC symbol + function: "map" # The "map" function is invoked with one input (the annotation SYMBOL), + args: # and one named argument, the mapping file (fixed for all variants) + filename: "hgnc_symbol_to_entrez_id.tsv" + on_missing: default # When no Entrez id is not for a symbol, the value is set to 0 + default: 0 + + Center: # Sequencing or processing center name + input: + - set: "constant" # The value is defined on the (optional) command-line arguments + column: "Center" # The argument is --Center + on_missing: default + default: "BIH" # When missing, the value "BIH" is used. + + NCBI_Build: + input: + - set: "constant" + column: "NCBI_Build" + on_missing: default + default: "GRCh37" + + Chromosome: # Sequence name + input: + - set: "fixed" # The input is taken from the vcf fixed field "CHROM" + column: "CHROM" + on_missing: stop # This field must be present. When absent, the program stops with an error + + Start_Position: # Position of the start of the variant. + input: # Note that vcf2maf.pl transforms the variant (position & allele sequences) + - set: "fixed" # to minimize them (see https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html). + column: "POS" # This is *NOT* compatible with variant normalization as defined in + on_missing: stop # https://genome.sph.umich.edu/wiki/Variant_Normalization + - set: "variant" # The function "minimize_mutation" performs variant minimization, + column: "REF" # so the output is (should be) identical to anything produced by vcf2maf.pl + on_missing: stop # If the user wants to keep the variant definition as in the vcf file, + - set: "variant" # the configuration should be updated, and the "Start_Position" column should be + column: "ALT" # defined similarly to the "Chromosome" column, simply copying the contents of + on_missing: stop # the vcf's "POS" column. + function: "minimize_mutation" # The same applies to the columns describing the reference & alternate allele sequences, + args: # "Reference_Allele", "Tumor_Seq_Allele1" & "Tumor_Seq_Allele2", which should be + return_value: "pos" # copied from vcf columns "REF", "REF" & "ALT" respectively. + on_missing: stop + + End_Position: # Position of the end of the variant + input: # This information is missing from the vcf + - set: "fixed" # It is reconstituted from the start position, and the lengths of the reference & alternative alleles + column: "POS" # The program stop if either values are missing. + on_missing: stop + - set: "variant" # If the user want to keep the variant definition as in the vcf file, + column: "REF" # another function is provided, which doesn't alter the variant's starting position, + on_missing: stop # and simply computes the end of the variant locus as: + - set: "variant" # POS + length(reference allele sequence) - 1 for substitutions & deletions, and + column: "ALT" # POS + 1 for insertions + on_missing: stop + function: "minimize_mutation" # This alternative function is "calc_end_pos". + args: # It takes the same input as "minimize_mutation", but with additional arguments. + return_value: "end" # "calc_end_pos" assumes that the variant is normalized. + on_missing: stop + + Strand: + input: + - set: "constant" + column: "Strand" + on_missing: default + default: "+" + + Variant_Classification: # Variant classification + input: # Maps the VEP variant classification defined in + - set: "annotation" # https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html#consequences + column: "Consequence" # to the cBioPortal/TCGA/GDC set of consequences defined in + - set: "annotation" # https://docs.gdc.cancer.gov/Encyclopedia/pages/Mutation_Annotation_Format_TCGAv2/ + column: "VARIANT_CLASS" # Additional mapping values & methods were taken directly from the vcf2maf.pl code in + - set: "variant" # routine GetVariantClassification (https://github.com/mskcc/vcf2maf hash d13e404 2022-11-02) + column: "REF" + - set: "variant" # Note that a simple mapping was not possible, because the algorithm requires + column: "ALT" # the knowledge of substitution, insertion or deletion to assign some values. + function: "variant_classification" + on_missing: default + default: "" + + Variant_Type: # Variant type (SNP/DNP/TNP/ONP/INS/DEL). + input: # The type "Consolidated" is not implemented. + - set: "variant" + column: "REF" # The function "variant_type" outputs the type based only on the length of + - set: "variant" # reference & alternative allele sequences. + column: "ALT" + function: "variant_type" + on_missing: default + default: "" + + Reference_Allele: # Reference allele (should be identical to the reference genome at the locus) + input: # Rather, it is taken from the normal homozygous allele. + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "REF" column is simply copied + column: "REF" # to the output column ("Reference_Allele"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "ref" + on_missing: stop + + Tumor_Seq_Allele1: # Unmutated allele in the tumor sample + input: + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "REF" column is simply copied + column: "REF" # to the output column ("Tumor_Seq_Allele1"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "ref" + on_missing: stop + + Tumor_Seq_Allele2: # Mutated allele in the tumor sample + input: + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "ALT" column is simply copied + column: "REF" # to the output column ("Tumor_Seq_Allele2"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "alt" + on_missing: stop + + dbSNP_RS: # dbSNP references + input: # Note that VEP also includes COSMIC references in that field. + - set: "annotation" # TODO: create a function that parses the vcf field, extracts only the dbSNP + column: "Existing_variation" # ids and collapses them into a single strings separated by semicolumns. + on_missing: default + default: "novel" + + dbSNP_Val_Status: + input: + - set: "constant" + column: "dbSNP_Val_Status" + on_missing: default + default: "" + + Tumor_Sample_Barcode: + input: + - set: "constant" + column: "tumor_id" + on_missing: default + default: "tumor" + + Matched_Normal_Sample_Barcode: + input: + - set: "constant" + column: "normal_id" + on_missing: default + default: "normal" + + Match_Norm_Seq_Allele1: # Match normal allele1. + input: # Should be identical to "Tumor_Allele1", but instead is set to the reference genome sequence + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "REF" column is simply copied + column: "REF" # to the output column ("Tumor_Seq_Allele1"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "ref" + on_missing: stop + + Match_Norm_Seq_Allele2: # Match normal allele2 (the allele mutated in the tumor) + input: + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "REF" column is simply copied + column: "REF" # to the output column ("Tumor_Seq_Allele1"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "ref" + on_missing: stop + + Tumor_Validation_Allele1: # Validation not implemented. All fields are empty + input: + - set: "constant" + column: "Tumor_Validation_Allele1" + on_missing: default + default: "" + + Tumor_Validation_Allele2: # Validation not implemented. All fields are empty + input: + - set: "constant" + column: "Tumor_Validation_Allele2" + on_missing: default + default: "" + + Match_Norm_Validation_Allele1: # Validation not implemented. All fields are empty + input: + - set: "constant" + column: "Match_Norm_Validation_Allele1" + on_missing: default + default: "" + + Match_Norm_Validation_Allele2: # Validation not implemented. All fields are empty + input: + - set: "constant" + column: "Match_Norm_Validation_Allele1" + on_missing: default + default: "" + + Verification_Status: + input: + - set: "constant" + column: "Verification_Status" + on_missing: default + default: "Unknown" + + Validation_Status: + input: + - set: "constant" + column: "Validation_Status" + on_missing: default + default: "Unknown" + + Mutation_Status: + input: + - set: "constant" + column: "Mutation_Status" + on_missing: default + default: "Somatic" + + Sequencing_Phase: + input: + - set: "constant" + column: "Sequencing_Phase" + on_missing: default + default: "Unknown" + + Sequence_Source: + input: + - set: "constant" + column: "Sequence_Source" + on_missing: default + default: "Unknown" + + Validation_Method: + input: + - set: "constant" + column: "Validation_Method" + on_missing: default + default: "Unknown" + + Score: + input: + - set: "constant" + column: "Score" + on_missing: default + default: "" + + BAM_File: + input: + - set: "constant" + column: "BAM_File" + on_missing: default + default: "" + + Sequencer: + input: + - set: "constant" + column: "Sequencer" + on_missing: default + default: "" + + Tumor_Sample_UUID: + input: + - set: "constant" + column: "Tumor_Sample_UUID" + on_missing: default + default: "" + + Matched_Norm_Sample_UUID: + input: + - set: "constant" + column: "Matched_Norm_Sample_UUID" + on_missing: default + default: "" + + # Start of supplementary columns not defined in ----------------------------------------------- + # https://docs.gdc.cancer.gov/Encyclopedia/pages/Mutation_Annotation_Format_TCGAv2/ ----------- + + # The columns belows are all defined in ------------------------------------------------------- + # https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/#notes-about-gdc-maf-implementation + # Note that some columns are commented out, and will not be part of the output. --------------- + + HGVSc: + input: + - set: "annotation" + column: "HGVSc" + on_missing: default + default: "" + + HGVSp: + input: + - set: "annotation" + column: "HGVSp" + on_missing: default + default: "" + + HGVSp_Short: # Short version of the protein mutation defined in + input: # VEP annotation column "HGVSp" + - set: "annotation" + column: "HGVSp" # The function "parse_protein_mutation" removed the + function: "parse_protein_mutation" # sequence identifier, and replaces 3-letter amino-acid codes + args: # with single letter amino-acid codes. + add_sequence: False # The arguments "add_sequence", "want_short" & "want_long" + want_short: True # allow the user to change this behaviour. + want_long: False + on_missing: skip + # default: "" + + Transcript_ID: + input: + - set: "annotation" + column: "Feature" + on_missing: default + default: "" + + Exon_Number: # VEP annotates the exon number & the total number of exons in the transcript. + input: # It is unclear what the MAF documentation requires. + - set: "annotation" + column: "EXON" + on_missing: default + default: "" + + t_depth: # Read depth in the tumor sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "tumor" + column: "DP" + on_missing: default + default: "" + + t_ref_count: # Reference allele read counts in the tumor sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "tumor" + column: "AD[REF]" + on_missing: default + default: "" + + t_alt_count: # Alternative allele read counts in the tumor sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "tumor" + column: "AD[0]" + on_missing: default + default: "" + + n_depth: # Read depth in the normal sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "normal" + column: "DP" + on_missing: default + default: "" + + n_ref_count: # Reference allele read counts in the normal sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "normal" + column: "AD[REF]" + on_missing: default + default: "" + + n_alt_count: # Alternative allele read counts in the normal sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "normal" + column: "AD[0]" + on_missing: default + default: "" + + Protein_Position: + input: + - set: "annotation" + column: "Protein_position" + on_missing: default + default: "" + + SWISSPROT: + input: + - set: "annotation" + column: "SWISSPROT" + on_missing: default + default: "" + function: "strip_sequence_version" + + # The columns below are not mentioned at all in the cBioPortal documentation ------------------ + # (https://docs.cbioportal.org/file-formats/#mutation-data) ----------------------------------- + # They are displayed in the order they are found in the GDC documentation, -------------------- + # except for "Protein_Position" & "SWISSPROT" which are mentioned as -------------------------- + # optional columns in cBioPortal. ------------------------------------------------------------- + + # all_effects + + Allele: + input: + - set: "annotation" + column: "Allele" + on_missing: default + default: "" + Gene: + input: + - set: "annotation" + column: "Gene" + on_missing: default + default: "" + Feature: + input: + - set: "annotation" + column: "Feature" + on_missing: default + default: "" + Feature_type: + input: + - set: "annotation" + column: "Feature_type" + on_missing: default + default: "" + # Consequence + cDNA_position: + input: + - set: "annotation" + column: "cDNA_position" + on_missing: default + default: "" + CDS_position: + input: + - set: "annotation" + column: "CDS_position" + on_missing: default + default: "" + Amino_acids: + input: + - set: "annotation" + column: "Amino_acids" + on_missing: default + default: "" + Codons: + input: + - set: "annotation" + column: "Codons" + on_missing: default + default: "" + Existing_variation: + input: + - set: "annotation" + column: "Existing_variation" + on_missing: default + default: "" + # ALLELE_NUM + DISTANCE: + input: + - set: "annotation" + column: "DISTANCE" + on_missing: default + default: "" + STRAND_VEP: + input: + - set: "annotation" + column: "STRAND" + on_missing: default + default: "" + SYMBOL: + input: + - set: "annotation" + column: "SYMBOL" + on_missing: default + default: "" + SYMBOL_SOURCE: + input: + - set: "annotation" + column: "SYMBOL_SOURCE" + on_missing: default + default: "" + HGNC_ID: + input: + - set: "annotation" + column: "HGNC_ID" + on_missing: default + default: "" + BIOTYPE: + input: + - set: "annotation" + column: "BIOTYPE" + on_missing: default + default: "" + CANONICAL: + input: + - set: "annotation" + column: "CANONICAL" + on_missing: default + default: "" + CCDS: + input: + - set: "annotation" + column: "CCDS" + on_missing: default + default: "" + ENSP: + input: + - set: "annotation" + column: "ENSP" + on_missing: default + default: "" + TREMBL: + input: + - set: "annotation" + column: "TREMBL" + on_missing: default + default: "" + UNIPARC: + input: + - set: "annotation" + column: "UNIPARC" + on_missing: default + default: "" + # RefSeq + SIFT: + input: + - set: "annotation" + column: "SIFT" + on_missing: default + default: "" + Polyphen: + input: + - set: "annotation" + column: "Polyphen" + on_missing: default + default: "" + EXON: + input: + - set: "annotation" + column: "EXON" + on_missing: default + default: "" + INTRON: + input: + - set: "annotation" + column: "INTRON" + on_missing: default + default: "" + DOMAINS: + input: + - set: "annotation" + column: "DOMAINS" + on_missing: default + default: "" + AF: + input: + - set: "annotation" + column: "AF" + on_missing: default + default: "" + AFR_AF: + input: + - set: "annotation" + column: "AFR_AF" + on_missing: default + default: "" + AMR_AF: + input: + - set: "annotation" + column: "AMR_AF" + on_missing: default + default: "" + # ASN_AF + EAS_AF: + input: + - set: "annotation" + column: "EAS_AF" + on_missing: default + default: "" + EUR_AF: + input: + - set: "annotation" + column: "EUR_AF" + on_missing: default + default: "" + SAS_AF: + input: + - set: "annotation" + column: "SAS_AF" + on_missing: default + default: "" + AA_AF: + input: + - set: "annotation" + column: "AA_AF" + on_missing: default + default: "" + EA_AF: + input: + - set: "annotation" + column: "EA_AF" + on_missing: default + default: "" + CLIN_SIG: + input: + - set: "annotation" + column: "CLIN_SIG" + on_missing: default + default: "" + SOMATIC: + input: + - set: "annotation" + column: "SOMATIC" + on_missing: default + default: "" + PUBMED: + input: + - set: "annotation" + column: "PUBMED" + on_missing: default + default: "" + MOTIF_NAME: + input: + - set: "annotation" + column: "MOTIF_NAME" + on_missing: default + default: "" + MOTIF_POS: + input: + - set: "annotation" + column: "MOTIF_POS" + on_missing: default + default: "" + HIGH_INF_POS: + input: + - set: "annotation" + column: "HIGH_INF_POS" + on_missing: default + default: "" + MOTIF_SCORE_CHANGE: + input: + - set: "annotation" + column: "MOTIF_SCORE_CHANGE" + on_missing: default + default: "" + IMPACT: + input: + - set: "annotation" + column: "IMPACT" + on_missing: default + default: "" + # PICK + VARIANT_CLASS: + input: + - set: "annotation" + column: "VARIANT_CLASS" + on_missing: default + default: "" + TSL: + input: + - set: "annotation" + column: "TSL" + on_missing: default + default: "" + HGVS_OFFSET: + input: + - set: "annotation" + column: "HGVS_OFFSET" + on_missing: default + default: "" + PHENO: + input: + - set: "annotation" + column: "PHENO" + on_missing: default + default: "" + # MINIMISED + GENE_PHENO: + input: + - set: "annotation" + column: "GENE_PHENO" + on_missing: default + default: "" + # FILTER + # flanking_bps + # vcf_id + # vcf_qual + gnomAD_AF: + input: + - set: "annotation" + column: "gnomAD_AF" + on_missing: default + default: "" + gnomAD_AFR_AF: + input: + - set: "annotation" + column: "gnomAD_AFR_AF" + on_missing: default + default: "" + gnomAD_AMR_AF: + input: + - set: "annotation" + column: "gnomAD_AMR_AF" + on_missing: default + default: "" + gnomAD_ASJ_AF: + input: + - set: "annotation" + column: "gnomAD_ASJ_AF" + on_missing: default + default: "" + gnomAD_EAS_AF: + input: + - set: "annotation" + column: "gnomAD_EAS_AF" + on_missing: default + default: "" + gnomAD_FIN_AF: + input: + - set: "annotation" + column: "gnomAD_FIN_AF" + on_missing: default + default: "" + gnomAD_NFE_AF: + input: + - set: "annotation" + column: "gnomAD_NFE_AF" + on_missing: default + default: "" + gnomAD_OTH_AF: + input: + - set: "annotation" + column: "gnomAD_OTH_AF" + on_missing: default + default: "" + gnomAD_SAS_AF: + input: + - set: "annotation" + column: "gnomAD_SAS_AF" + on_missing: default + default: "" + diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml new file mode 100644 index 000000000..8a155a981 --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml @@ -0,0 +1,7 @@ +channels: +- bioconda +- conda-forge +dependencies: +- python >=3.8 +- vcfpy +- ruamel.yaml diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/exceptions.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/exceptions.py new file mode 100644 index 000000000..0e92f1692 --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/exceptions.py @@ -0,0 +1,22 @@ +class IllegalValue(Exception): + """Illegal value found during parsing""" + + pass + + +class MissingValue(Exception): + """Missing value found during parsing""" + + pass + + +class ActionStop(Exception): + """Interrupting parsing upon missing value or parsing error""" + + pass + + +class FunctionError(Exception): + """Error encountered during function""" + + pass diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/functions.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/functions.py new file mode 100644 index 000000000..216e27cfb --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/functions.py @@ -0,0 +1,161 @@ +import importlib.util +import inspect +import logging +import os +import re +import typing + +from common_functions import calc_end_pos, minimize_mutation, strip_sequence_version, variant_type +import exceptions +from protein_mutation_parser import parse_protein_mutation +from variant_classification import variant_classification + +# from action import Action + + +class Functions: + mapping_files = {} + TAB = re.compile("\t") + + def __init__(self, config: typing.Dict[str, typing.Any]): + self.compiled = Functions.importCode(config["functions"]) if "functions" in config else {} + self.compiled["identity"] = Functions.identity + self.compiled["map"] = Functions.mapper + + self.compiled["minimize_mutation"] = minimize_mutation + self.compiled["calc_end_pos"] = calc_end_pos + self.compiled["strip_sequence_version"] = strip_sequence_version + self.compiled["variant_type"] = variant_type + self.compiled["parse_protein_mutation"] = parse_protein_mutation + self.compiled["variant_classification"] = variant_classification + + for col_name, col_def in config["output"].items(): + if "function" in col_def and not col_def["function"] in self.compiled: + raise exceptions.MissingValue( + 'Function "{}" requested to process column "{}" not found'.format( + col_def["function"], col_name + ) + ) + + @staticmethod + def importCode(functions, module_name="extra_functions"): + """Read & compile processing functions from python files + + :param functions: list of python files to compile + :return: a dict of compiled functions as values, with the function names as keys + """ + to_compile = [] + for filename in functions: + with open(filename, "rt") as f: + code = f.read() + to_compile.append(code) + logging.info('Loaded additional function(s) from file "{}"'.format(filename)) + + spec = importlib.util.spec_from_loader(module_name, loader=None) + module = importlib.util.module_from_spec(spec) + exec("\n\n".join(to_compile), module.__dict__) + globals()[module_name] = module + + hooks = dict(inspect.getmembers(module, inspect.isfunction)) + logging.debug("Functions: {}".format(hooks.keys())) + return hooks + + @staticmethod + def identity(value, args: typing.Dict[str, typing.Any] = None): + if value is None: + return None + assert isinstance(value, list) + assert len(value) == 1 + result = value[0] + + return result + + @staticmethod + def mapper(value, args: typing.Dict[str, typing.Any] = None): + if args is None or not isinstance(args, dict) or "filename" not in args: + raise exceptions.MissingValue("Missing mapping filename argument") + filename = os.path.realpath(os.path.join(os.path.dirname(__file__), args["filename"])) + + if value is None: + return None + assert isinstance(value, list) + assert len(value) == 1 + value = value[0] + if value is None: + return None + + if filename not in Functions.mapping_files: + m = {} + with open(filename, "rt") as f: + for line in f: + try: + k, v = Functions.TAB.split(line.strip(), 1) + m[k] = v + except Exception: + pass + Functions.mapping_files[filename] = m + m = Functions.mapping_files[filename] + + return [m.get(v, None) for v in value] + + @staticmethod + def max_length(previous: int = 0, current: int = 0) -> int: + if current == 0: + return previous + if previous < 2: + return current + if current == 1: + return previous + if current != previous: + raise exceptions.IllegalValue( + "Record expansion impossible: previous length = {}, current length = {}".format( + previous, current + ) + ) + return current + + def run( + self, + values, + fct: str = "identity", + args: typing.Dict[str, typing.Any] = None, + default: str = None, + ): + if values is None: + return None + assert isinstance(values, list) + alts = {} + for value in values: + if value is None: + continue + assert isinstance(value, dict) + for k, v in value.items(): + if k not in alts: + alts[k] = 0 + if v is None: + continue + assert isinstance(v, list) and len(v) > 0 + alts[k] = Functions.max_length(alts[k], len(v)) + + f = self.compiled[fct] + + results = {} + for alt in alts: + x = [] + for value in values: + assert value is None or value[alt] is None or isinstance(value[alt], list) + x.append(value[alt]) + try: + results[alt] = f(x, args) + except Exception as e: + logging.error('Function "{}" has returned error {}'.format(fct, e)) + # raise exceptions.FunctionError( + # 'Error in function "{}" for value {} and arguments {}'.format(fct, x, args) + # ) + results[alt] = None + if results[alt] is None: + results[alt] = default + if results[alt] is not None and not isinstance(results[alt], list): + results[alt] = [results[alt]] + + return results diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/parser.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/parser.py new file mode 100644 index 000000000..6c2410732 --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/parser.py @@ -0,0 +1,427 @@ +import logging +import re +import typing + +from annotation import Annotation +import exceptions +import vcfpy + + +class VcfParser: + pattern = re.compile("^([^\[\]\s]+)(\[([0-9]+|REF)\])?$") # noqa: W605 + + def __init__( + self, + config: typing.Dict[str, typing.Any], + header: vcfpy.Header, + samples: typing.Dict[str, str], + ): + """Create the parser for column requests + + The parser is configured using the configuration yaml file, in particular the "annotation" dict, + and the info & format list of requested IDs. + The latter is used to give the user control of the set of INFO & FORMAT IDs that can be used in parsing. + When these lists are missing from the configuration, all the INFO & FORMAT IDs present in the VCF can be used. + + The annotation defines the extraction pattern for parsing the annotation field description in the VCF header. + The description field generally consists of a prefix, followed by the column names of the annotations. + The `extract` regular expression must define the column names as a single string in the first group, + and the `split` regular expression is used to separate the annotation field (in the header or in the records) + into individual values. + + The sample names must be provided as a dict with `tumor` and `normal` keys (the latter being optional). + This provides a mapping between logical labels (`tumor` & `normal`) and the sample column names. + + :param config: configuration dict + :param header: VCF header as vcfpy.Header object + :param samples: samples mapping dict + """ + if samples["normal"]: + if not samples["normal"] in header.samples.names: + raise exceptions.IllegalValue( + 'Normal sample "{}" not found in vcf header'.format(samples["normal"]) + ) + if samples["tumor"]: + if not samples["tumor"] in header.samples.names: + raise exceptions.IllegalValue( + 'Tumor sample "{}" not found in vcf header'.format(samples["tumor"]) + ) + self.samples = samples + + self.annotation = None + self.infos = VcfParser._get_id_list(config.get("info", None), header, "INFO") + self.formats = VcfParser._get_id_list(config.get("format", None), header, "FORMAT") + + if ( + "annotation" in config + and isinstance(config["annotation"], dict) + and set(["id", "extract", "split"]) <= set(config["annotation"].keys()) + ): + self.annotation = Annotation( + annotation_id=config["annotation"]["id"], + allele_column=config["annotation"]["allele"] + if "allele" in config["annotation"] + else None, + extract=config["annotation"]["extract"], + split=config["annotation"]["split"], + ) + self.annotation.parseHeader(header) + + self.constants = {} + + def addConstant(self, key, value): + """Add an key, value pair to the parser set of constant values + + :param key: name of the constant column + :param value: value of all elements in the constant column + """ + if key in self.constants: + logging.warning( + 'Value of constant "{}" is replaced from {} to {}'.format( + key, self.constants[key], value + ) + ) + self.constants[key] = value + + @staticmethod + def _get_id_list( + request, header, line_type="" + ) -> typing.Dict[str, vcfpy.header.CompoundHeaderLine]: + """Creates a dict of FORMAT or INFO lines + + The user can subset the ID found in the vcf using the configuration file. + If a list of requested IDs is provided, these IDs will be checked for presence in the VCF. + If any requested ID are missing from the VCF, an exception is raised. + If there is no user request, all IDs present in the VCF header are returned. + + :param request: list of ids, possibly empty or None + :param header: VCF header as vcfpy object + :param line_type: either INFO or FORMAT. Other values trigger an exception + :return: dict with ID as keys, and header lines as values (vcfpy.CompoundHeaderLine) + """ + if line_type == "INFO": + ids = header.info_ids() + value_fct = header.get_info_field_info + elif line_type == "FORMAT": + ids = header.format_ids() + value_fct = header.get_format_field_info + else: + raise exceptions.IllegalValue('Illegal VCF header line "{}"'.format(line_type)) + id_list = {x: value_fct(x) for x in ids} + if request: + request = set(request) + in_header = set(id_list.keys()) + missing = request - in_header + if len(missing) > 0: + raise exceptions.MissingValue( + 'Requested {} id(s) not found in vcf header: "{}"'.format( + '", "'.join(missing), '", "'.join(in_header) + ) + ) + unused = in_header - request + for field in unused: + del id_list[field] + return id_list + + def subset(self, record: vcfpy.Record, index=None) -> vcfpy.Record: + """Subset a VCF record to retain on one alt allele + + A new VCF record is created, to represent the ith alternative allele of the variant. + The allele selection is provided by the index (0 is the first alt allele). + When the index is None, the original VCF record is returned, with all the alternative alleles. + When the index is greater than the number of alt alleles found for the variant, + an empty record is returned (None). + + :param record: the VCF record with multiple variants + :param index: the index of the selected alt allele (starting from 0) + :return: the variant with only the selected alt allele, or an empty record when the ith allele is missing, or the original record if the index is missing + """ + if index is None: + return record + if index >= len(record.ALT): + return None + infos = {} + for ID in record.INFO.keys(): + assert ID in self.infos + header = self.infos[ID] + if header.number == vcfpy.header.HEADER_NUMBER_REF: + infos[ID] = [record.INFO[ID][0], record.INFO[ID][1 + index]] + elif header.number == vcfpy.header.HEADER_NUMBER_ALLELES: + infos[ID] = [record.INFO[ID][index]] + else: + infos[ID] = record.INFO[ID] + + formats = [] + for call in record.calls: + data = {} + for ID in record.FORMAT: + assert ID in self.formats + fmt = self.formats[ID] + if fmt.number == vcfpy.header.HEADER_NUMBER_REF: + data[ID] = [call.data[ID][0], call.data[ID][1 + index]] + elif fmt.number == vcfpy.header.HEADER_NUMBER_ALLELES: + data[ID] = [call.data[ID][index]] + else: + data[ID] = call.data[ID] + formats.append(vcfpy.record.Call(call.sample, data)) + + return vcfpy.record.Record( + record.CHROM, + record.POS, + record.ID, + record.REF, + [record.ALT[index]], + record.QUAL, + record.FILTER, + infos, + record.FORMAT, + formats, + ) + + def getInputValue( + self, + record: vcfpy.Record, + theSet: str, + theColumn: str, + theSample: str = None, + default: str = None, + ): + """Extract the requested value(s) from a VCF record + + The request format depends on the set of values the data must be extracted from. + The available sets are: + + - `constant`: constant values stored in the parser (typically the genome release, or the organisation name). + The request must be the constant name. + - `fixed`: the fixed columns of the VCF. The request must be one of `CHROM`, `POS`, ÌD`, `QUAL` or `FILTER`. + - `variant`: the reference or alternative variant. The request must be `REF` or `ALT`, or `ALT[]`. + If the request is `ALT`, then all alt variants will be returned. + If the request is `ALT[]`, then only the ith variant is returned, and if there is no ith variant, None is returned. + - `info`: an INFO field, by ID. The request must be ``, `[]` or `[REF]`. + The meaning of the index (either a positive integer, starting from 0, or `REF`) depends on the + INFO field numbering scheme, as defined in the VCF header. + When the number of values depends on the number of alt alleles (either `R` or `A` in VCF Number parlance), + only one value can be returned. If the value list contains the reference (`R` number of values), + the value for the reference can be obtained using the `REF` index. + Alternatively, when the number of values does not depend on the number of alt alleles, + then the indexing can be used. When it isn't used, all values are returned. + - `format`: a `FORMAT` field, by ID. The request format is identical to the format used for `INFO` fields, + but the logical sample id (either `tumor` or `normal`) must be provided. + - `annotation`: an annotation field, by column name. The request format is identical to the format used for `INFO` fields. + When annotations have been configured to extract the allele from the annotation columns, then + the annotations are assumed to have a `A` number, so they are attached to alt alleles. No indexing is possible. + If it is not the case, the annotations can have any number of values. Indexing by number is possible. + + The returned values are either a list (of length 1 for `constant` and `fixed` sets), or a dict of lists + when the requested values depend on the alt allele. In that case, the lists lengths are always 1 for + `INFO` and `FORMAT` fields, but can be longer for annotations (as there can be multiple annotations per alt allele). + + :param record: the VCF record the data is extracted from, as a vcfpy.Record object + :param theSet: one of `constant`, `fixed`, `variant`, `info`, `format` or `annotation`, to describe the type of data for extraction + :param theColumn: the column ID, possibly with indexing + :param theSample: sample logical label (`tumor` or `normal`), for `format` data extraction + :param action: action to be taken for missing values. One of `ignore`, `skip`, `stop`, `default`. + :return: the parsed values, as a dict for alt-allele dependent values, or a list otherwise, or None when absent + """ + if record is None: + raise exceptions.MissingValue("No record provided") + if not theSet or not theColumn: + raise exceptions.MissingValue( + 'Missing set or column information for record "{}"'.format(record) + ) + if theSet == "format": + if not theSample: + raise exceptions.MissingValue( + 'Missing sample information for column "{}" and record "{}"'.format( + theColumn, record + ) + ) + if theSample not in self.samples: + raise exceptions.IllegalValue('Unknown sample "{}"'.format(theSample)) + theSample = self.samples[theSample] + + value = None + if theSet == "constant": + if theColumn in self.constants: + value = self.constants.get(theColumn, None) + if value is not None: + value = VcfParser._expandUnique(value, record.ALT) + elif theSet == "fixed": + value = VcfParser._expandUnique(VcfParser._getFixed(record, theColumn), record.ALT) + elif theSet == "variant": + value = VcfParser._getVariant(record, theColumn) + elif theSet == "info": + numbers = {x.id: x.number for x in self.infos.values()} + infos = VcfParser._expandDict(record.INFO, record.ALT, numbers) + value = self._getRequest(theColumn, infos, numbers) + elif theSet == "format": + if theSample: + numbers = {x.id: x.number for x in self.formats.values()} + formats = VcfParser._expandDict( + record.call_for_sample[theSample].data, record.ALT, numbers + ) + value = self._getRequest(theColumn, formats, numbers) + elif theSet == "annotation": + numbers = {x: vcfpy.header.HEADER_NUMBER_UNBOUNDED for x in self.annotation.columns} + annotations = self.annotation.getAnnotations(record) + value = self._getRequest(theColumn, annotations, numbers) + else: + raise exceptions.IllegalValue('Unknown set "{}"'.format(theSet)) + + if default is not None: + value = VcfParser._insert_default(value, default, [alt.value for alt in record.ALT]) + else: + assert value is None or isinstance(value, dict) + if isinstance(value, dict): + for k, v in value.items(): + assert v is None or isinstance(v, list) + + return value + + @staticmethod + def _insert_default(value: typing.Dict[str, typing.Any], default: str, alts: typing.List[str]): + if value is None: + value = {alt: [default] for alt in alts} + else: + assert isinstance(value, dict) + for alt in alts: + if alt in value: + if value[alt] is None: + value[alt] = [default] + else: + assert isinstance(value[alt], list) + for i in range(len(value[alt])): + if value[alt][i] is None: + value[alt][i] = default + return value + + @staticmethod + def _expandUnique( + value, alts: typing.List[vcfpy.record.AltRecord] + ) -> typing.Dict[str, typing.Any]: + if value is None: + return {alt.value: value for alt in alts} + else: + return {alt.value: [value] for alt in alts} + + @staticmethod + def _expandDictElement( + value, alts: typing.List[vcfpy.record.AltRecord], number + ) -> typing.Dict[str, typing.Any]: + if value is None: + return None + if not isinstance(value, list): + return {alt.value: [value] for alt in alts} + if number == vcfpy.header.HEADER_NUMBER_UNBOUNDED: + return {alt.value: value for alt in alts} + if number == vcfpy.header.HEADER_NUMBER_ALLELES: + return {alts[i].value: [value[i]] for i in range(len(alts))} + if number == vcfpy.header.HEADER_NUMBER_REF: + result = {alts[i].value: [value[i + 1]] for i in range(len(alts))} + result["__REF__"] = [value[0]] + return result + return {alt.value: value for alt in alts} + + @staticmethod + def _expandDict( + value, alts: typing.List[vcfpy.record.AltRecord], numbers + ) -> typing.Dict[str, typing.Dict[str, typing.Any]]: + if value is None: + return None + return {k: VcfParser._expandDictElement(v, alts, numbers[k]) for k, v in value.items()} + + @staticmethod + def _getFixed(record: vcfpy.Record, theColumn: str) -> typing.List[typing.Any]: + """Extract the fixed part of a vcf record + + The variant position (CHROM & POS), its identifier (ID), filter (FILTER) & quality (QUAL) values can be returned. + The allowed column values are: CHROM, POS, ID, FILTER & QUAL. + Note that multiple IDs & multiple filters are collapsed into a single string with the semicolumn (;) as separator + + :param record: vcf record as vcfpy.Record object + :param theColumn: which fixed value must be returned + :return: an array of length 1 with the requested fixed value + """ + if theColumn == "CHROM": + return record.CHROM + elif theColumn == "POS": + return record.POS + elif theColumn == "ID": + return ";".join(record.ID) + elif theColumn == "QUAL": + return record.QUAL + elif theColumn == "FILTER": + return ";".join(record.FILTER) + else: + raise exceptions.IllegalValue('Unknown fixed column "{}"'.format(theColumn)) + + @staticmethod + def _getVariant(record: vcfpy.Record, theColumn: str) -> typing.Dict[str, typing.List[str]]: + """Extract the reference and alternative allele(s) from a vcf record + + A single reference & possibly multiple alternative alleles are returned as a list. + The allowed column names are 'REF' for the reference, and + 'ALT' for the first alt allele,'ALT[]' for the nth, or 'ALT[*]' for all the alt alleles. + Note that 'ALT[]' will return an empty list in the requested number is larger than the number of alternative alleles for the variant. + + :param record: vcf record as vcfpy.Record object + :param theColumn: the type of allele list to be returned + :return: a dict of lists of length 1 for the reference allele, or a possibly longer list for alternative alleles + """ + if theColumn == "REF": + return {alt.value: [record.REF] for alt in record.ALT} + m = VcfParser.pattern.match(theColumn) + if not m: + raise exceptions.IllegalValue('Unknown variant column "{}"'.format(theColumn)) + groups = m.groups() + if groups[0] != "ALT": + raise exceptions.IllegalValue('Unknown variant column "{}"'.format(theColumn)) + if groups[2]: + value = {alt.value: None for alt in record.ALT} + n = int(groups[2]) + if n < len(record.ALT): + value[record.ALT[n].value] = [record.ALT[n].value] + return value + else: + return {alt.value: [alt.value] for alt in record.ALT} + + def _getRequest( + self, + request: str, + values: typing.Any, # A dict with alt alleles as keys and with data relevant to the allele as value + numbers: typing.Dict[str, str], + ) -> typing.Dict[str, typing.Any]: + if values is None: + return None + + m = VcfParser.pattern.match(request) + if not m: + raise exceptions.IllegalValue('Syntax error in column request "{}"'.format(request)) + + groups = m.groups() + theColumn = groups[0] + if theColumn not in values.keys(): + return None + result = values[theColumn] + + if groups[2]: + if groups[2] == "REF": + if numbers[theColumn] != vcfpy.header.HEADER_NUMBER_REF: + raise exceptions.IllegalValue( + 'Requested data for reference allele in column "{}" which doesn\'t contain it'.format( + theColumn + ) + ) + assert "__REF__" in result + ref_data = result.pop("__REF__") + for alt in result.keys(): + result[alt] = ref_data + else: + n = int(groups[2]) + for alt, v in result.items(): + if n < len(v) and v[n] is not None: + result[alt] = [v[n]] + else: + result[alt] = None + + return result diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py new file mode 100644 index 000000000..9b60c721e --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py @@ -0,0 +1,433 @@ +import functools +import re + + +class ProteinMutationFormatException(Exception): + pass + + +aa_codes_short = ( + "A", + "C", + "D", + "E", + "F", + "G", + "H", + "I", + "K", + "L", + "M", + "N", + "P", + "Q", + "R", + "S", + "T", + "V", + "W", + "Y", + "B", + "Z", + "X", +) + +aa_codes_long = ( + "Ala", + "Cys", + "Asp", + "Glu", + "Phe", + "Gly", + "His", + "Ile", + "Lys", + "Leu", + "Met", + "Asn", + "Pro", + "Gln", + "Arg", + "Ser", + "Thr", + "Val", + "Trp", + "Tyr", + "Asx", + "Glx", + "Xaa", +) + +long_to_short = { + "Ala": "A", + "Cys": "C", + "Asp": "D", + "Glu": "E", + "Phe": "F", + "Gly": "G", + "His": "H", + "Ile": "I", + "Lys": "K", + "Leu": "L", + "Met": "M", + "Asn": "N", + "Pro": "P", + "Gln": "Q", + "Arg": "R", + "Ser": "S", + "Thr": "T", + "Val": "V", + "Trp": "W", + "Tyr": "Y", + "Asx": "B", + "Glx": "Z", + "Xaa": "X", + "Ter": "*", + "A": "A", + "C": "C", + "D": "D", + "E": "E", + "F": "F", + "G": "G", + "H": "H", + "I": "I", + "K": "K", + "L": "L", + "M": "M", + "N": "N", + "P": "P", + "Q": "Q", + "R": "R", + "S": "S", + "T": "T", + "V": "V", + "W": "W", + "Y": "Y", + "B": "B", + "Z": "Z", + "X": "X", + "*": "*", + "=": "=", + "?": "?", +} + +short_to_long = { + "A": "Ala", + "C": "Cys", + "D": "Asp", + "E": "Glu", + "F": "Phe", + "G": "Gly", + "H": "His", + "I": "Ile", + "K": "Lys", + "L": "Leu", + "M": "Met", + "N": "Asn", + "P": "Pro", + "Q": "Gln", + "R": "Arg", + "S": "Ser", + "T": "Thr", + "V": "Val", + "W": "Trp", + "Y": "Tyr", + "B": "Asx", + "Z": "Glx", + "X": "Xaa", + "*": "Ter", + "Ala": "Ala", + "Cys": "Cys", + "Asp": "Asp", + "Glu": "Glu", + "Phe": "Phe", + "Gly": "Gly", + "His": "His", + "Ile": "Ile", + "Lys": "Lys", + "Leu": "Leu", + "Met": "Met", + "Asn": "Asn", + "Pro": "Pro", + "Gln": "Gln", + "Arg": "Arg", + "Ser": "Ser", + "Thr": "Thr", + "Val": "Val", + "Trp": "Trp", + "Tyr": "Tyr", + "Asx": "Asx", + "Glx": "Glx", + "Xaa": "Xaa", + "Ter": "Ter", + "=": "=", + "?": "?", +} + + +@functools.lru_cache +def _build_protein_pattern(): + prefix = "^(([A-z0-9_\.\(\)-]+):)?p\.\(?" # noqa: W605 + postfix = "\)?$" # noqa: W605 + + aa = "(" + "|".join(aa_codes_short) + "|" + "|".join(aa_codes_long) + ")" + aaTer = ( + "(" + + "|".join(aa_codes_short) + + "|" + + "|".join(aa_codes_long) + + "|\*|Ter" # noqa: W605 + + ")" + ) + aaAll = ( + "(" + + "|".join(aa_codes_short) + + "|" + + "|".join(aa_codes_long) + + "|\*|Ter|=|\?" # noqa: W605 + + ")" + ) + nb = "([0-9]+)" + nb_unknown = "([0-9]+|\?)" # noqa: W605 + + interval = aa + nb + "_" + aa + nb + one_or_interval = aa + nb + "(_" + aa + nb + ")?" + + substitution = aaTer + nb + aaAll + + deletion = one_or_interval + "del" + duplication = one_or_interval + "dup" + + insertion = interval + "ins" + "(" + aa + "*)" + aaTer + + delins = one_or_interval + "delins" + "(" + aa + "*)" + aaTer + + frameshift = aaTer + nb + aa + "fs" + "(Ter|\*)" + nb_unknown # noqa: W605 + + extensionN = "(Met|M)1" + "ext(-[0-9]+|\?)" # noqa: W605 + extensionC = "(Ter|\*)" + nb + aa + "ext" + "(Ter|\*)" + nb_unknown # noqa: W605 + + pattern = ( + prefix + + "(" + + "|".join( + [ + "0", # No group, but seq in 2 + substitution, # 3: ref, 4: position, 5: alt + duplication, # 6: start, 7: start pos, 9: end, 10: end pos + deletion, # 11: start, 12: start pos, 14: end, 15: end pos + insertion, # 16: start, 17: start pos, 18: end, 19: end pos (=start pos + 1), 20+22: insertion + delins, # 23: start, 24: start pos, 26: end, 27: end pos, 28+30: insertion + frameshift, # 31: start, 33: start pos, 33: end, 35: ter pos + extensionN, # 37: pos (negative number) + extensionC, # 39: pos, 40: alt, 42: ter pos + ] + ) + + ")" + + postfix + ) + + return re.compile(pattern) + + +def _aa(aa, want_short=True, want_long=False): + if want_short and aa in long_to_short.keys(): + return long_to_short[aa] + if want_long and aa in short_to_long.keys(): + return short_to_long[aa] + return aa + + +def _is_long(aa): + if aa not in long_to_short.keys(): + raise ProteinMutationFormatException("Unexpected AA code {}".format(aa)) + return len(aa) == 3 + + +def _many_aas(many_aas, want_short=True, want_long=False, is_long=False): + if not many_aas: + return "" + if not want_short and not want_long: + return many_aas + n = 3 if is_long else 1 + if want_short: + mapping = long_to_short + elif want_long: + mapping = short_to_long + else: + mapping = None + # print("DEBUG- _many_aas source = {} by {}".format(many_aas, n)) + i = 0 + converted = "" + while i < len(many_aas): + converted += mapping[many_aas[i : i + n]] + i += n + return converted + + +def _interval(groups, i0, want_short=True, want_long=False): + first_aa = _aa(groups[i0 + 0], want_short=want_short, want_long=want_long) + first_n = groups[i0 + 1] + last_aa = _aa(groups[i0 + 2], want_short=want_short, want_long=want_long) + last_n = groups[i0 + 3] + return first_aa + first_n + "_" + last_aa + last_n + + +def _one_or_interval(groups, i0, want_short=True, want_long=False): + one_aa = _aa(groups[i0 + 0], want_short=want_short, want_long=want_long) + one_n = groups[i0 + 1] + rslt = one_aa + one_n + if groups[i0 + 2] is not None: + interval_aa = _aa(groups[i0 + 3], want_short=want_short, want_long=want_long) + interval_n = groups[i0 + 4] + rslt += "_" + interval_aa + interval_n + return rslt + + +def _parse_mutation_groups(groups, want_short=True, want_long=False): + if groups[2] == "0": + rslt = "0" + + elif groups[3] is not None: + # Substitutions + rslt = ( + _aa(groups[3], want_short=want_short, want_long=want_long) + + groups[4] + + _aa(groups[5], want_short=want_short, want_long=want_long) + ) + # print("DEBUG- substitution: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(3, 6)]), rslt)) + + elif groups[6] is not None: + # Duplications + rslt = _one_or_interval(groups, 6, want_short=want_short, want_long=want_long) + "dup" + # print("DEBUG- duplication: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(6, 11)]), rslt)) + + elif groups[11] is not None: + # Deletions + rslt = _one_or_interval(groups, 11, want_short=want_short, want_long=want_long) + "del" + # print("DEBUG- deletion: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(11, 16)]), rslt)) + + elif groups[16] is not None: + # Insertions + is_long = _is_long(groups[16]) + rslt = ( + _interval(groups, 16, want_short=want_short, want_long=want_long) + + "ins" + + _many_aas(groups[20], want_short=want_short, want_long=want_long, is_long=is_long) + + _aa(groups[22], want_short=want_short, want_long=want_long) + ) + # print("DEBUG- insertion: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(16, 23)]), rslt)) + + elif groups[23] is not None: + # Deletion-insertions + is_long = _is_long(groups[23]) + rslt = ( + _one_or_interval(groups, 23, want_short=want_short, want_long=want_long) + + "delins" + + _many_aas(groups[28], want_short=want_short, want_long=want_long, is_long=is_long) + + _aa(groups[30], want_short=want_short, want_long=want_long) + ) + # print("DEBUG- delins: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(23, 31)]), rslt)) + + elif groups[31] is not None: + # Frameshift + rslt = ( + _aa(groups[31], want_short=want_short, want_long=want_long) + + groups[32] + + _aa(groups[33], want_short=want_short, want_long=want_long) + + "fs" + + _aa(groups[34], want_short=want_short, want_long=want_long) + + groups[35] + ) + # print("DEBUG- frameshift: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(31, 36)]), rslt)) + + elif groups[36] is not None: + # Extension N terminus + rslt = _aa(groups[36], want_short=want_short, want_long=want_long) + "1ext" + groups[37] + # print("DEBUG- extension N: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(36, 38)]), rslt)) + + elif groups[38] is not None: + # Extension C terminus + rslt = ( + _aa(groups[38], want_short=want_short, want_long=want_long) + + groups[39] + + _aa(groups[40], want_short=want_short, want_long=want_long) + + "ext" + + _aa(groups[41], want_short=want_short, want_long=want_long) + + groups[42] + ) + # print("DEBUG- extension C: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(38, 43)]), rslt)) + + return rslt + + +def _parse_one_mutation(mut, want_short=True, want_long=False, add_sequence=False): + if mut is None: + return "" + + # print("DEBUG- received mutation {}".format(mut)) + m = _build_protein_pattern().match(mut) + if not m: + raise ProteinMutationFormatException( + 'Protein mutation "{}" doesn\'t follow the HGVS nomenclature'.format(mut) + ) + groups = m.groups() + # print("DEBUG- mutation {} is valid, found groups are:".format(mut)) + # for i in range(len(groups)): + # if groups[i] is not None: + # print(" {}: {}".format(i, groups[i])) + + rslt = "p." + _parse_mutation_groups(groups, want_short=want_short, want_long=want_long) + + if add_sequence: + rslt = groups[1] + ":" + rslt + + return rslt + + +def parse_protein_mutation(x, args): + if x is None: + return None + assert isinstance(x, list) and len(x) == 1 + if x[0] is None: + return None + x = x[0] + + add_sequence = False + want_short = True + want_long = False + if args is not None and isinstance(args, dict): + add_sequence = args.get("add_sequence", add_sequence) + want_short = args.get("want_short", want_short) + want_long = args.get("want_long", want_long) + if want_short and want_long: + raise Exception("Cannot force both short & long amino-acide representations") + + rslts = [] + for mut in x: + try: + rslt = _parse_one_mutation( + mut, want_short=want_short, want_long=want_long, add_sequence=add_sequence + ) + rslts.append(rslt) + except ProteinMutationFormatException as e: + raise Exception(e) + + return rslts + + +def _test_re(x): + m = _build_protein_pattern().match(x) + if not m: + print('"{}" doesn\'t match'.format(x)) + else: + print('Groups of "{}":'.format(x)) + gs = m.groups() + for i in range(len(gs)): + if gs[i] is not None: + print(" {}: {}".format(i, gs[i])) + + +# with open("t", "rt") as f: +# for line in f: +# test_re(line.strip()) diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/variant_classification.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/variant_classification.py new file mode 100644 index 000000000..7d279c98e --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/variant_classification.py @@ -0,0 +1,125 @@ +# import exceptions +# from action import Action + + +# Mapping taken from vcftomaf.pl routine GetVariantClassification +# Github repo: https://github.com/mskcc/vcf2maf hash d13e404 2022-11-02 +# No change since tag 1.6.21 hash 754d68a 2021-04-24 +variant_classes_vcftomaf = ( + ("splice_acceptor_variant", "Splice_Site"), + ("splice_donor_variant", "Splice_Site"), + ("transcript_ablation", "Splice_Site"), + ("exon_loss_variant", "Splice_Site"), + ("stop_gained", "Nonsense_Mutation"), + # + ("stop_lost", "Nonstop_Mutation"), + ("initiator_codon_variant", "Translation_Start_Site"), + ("start_lost", "Translation_Start_Site"), + # + ("missense_variant", "Missense_Mutation"), + ("coding_sequence_variant", "Missense_Mutation"), + ("conservative_missense_variant", "Missense_Mutation"), + ("rare_amino_acid_variant", "Missense_Mutation"), + ("transcript_amplification", "Intron"), + ("intron_variant", "Intron"), + ("INTRAGENIC", "Intron"), + ("intragenic_variant", "Intron"), + ("splice_region_variant", "Splice_Region"), + ("incomplete_terminal_codon_variant", "Silent"), + ("synonymous_variant", "Silent"), + ("stop_retained_variant", "Silent"), + ("NMD_transcript_variant", "Silent"), + ("mature_miRNA_variant", "RNA"), + ("exon_variant", "RNA"), + ("non_coding_exon_variant", "RNA"), + ("non_coding_transcript_exon_variant", "RNA"), + ("non_coding_transcript_variant", "RNA"), + ("nc_transcript_variant", "RNA"), + ("5_prime_UTR_variant", "5'UTR"), + ("5_prime_UTR_premature_start_codon_gain_variant", "5'UTR"), + ("3_prime_UTR_variant", "3'UTR"), + ("TF_binding_site_variant", "IGR"), + ("regulatory_region_variant", "IGR"), + ("regulatory_region", "IGR"), + ("intergenic_variant", "IGR"), + ("intergenic_region", "IGR"), + ("upstream_gene_variant", "5'Flank"), + ("downstream_gene_variant", "3'Flank"), +) +# Missing from VEP 109 description +# https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html +variant_classes_vep109 = ( + ("splice_donor_5th_base_variant", "Splice_Region"), + ("splice_donor_region_variant", "Splice_Region"), + ("splice_polypyrimidine_tract_region", "Splice_Region"), + ("start_retained_variant", "Silent"), + ("TFBS_ablation", "IGR"), + ("TFBS_amplification", "IGR"), + ("regulatory_region_ablation", "IGR"), + ("regulatory_region_amplification", "IGR"), + ("feature_elongation", "Targeted_Region"), + ("feature_truncation", "Targeted_Region"), +) +variant_classes_all = variant_classes_vcftomaf + variant_classes_vep109 + + +def variant_classification(x, args=None): + if x is None: + return None + assert isinstance(x, list) and len(x) == 4 + if x[0] is None: + return None + assert isinstance(x[0], list) and len(x[0]) > 0 + if x[1] is None: + x[1] = [None] * len(x[0]) + assert isinstance(x[1], list) and len(x[1]) == len(x[0]) + assert isinstance(x[2], list) and len(x[2]) == len(x[0]) + assert isinstance(x[3], list) and len(x[3]) == len(x[0]) + tcga = list() + for i in range(len(x[0])): + ensembl = x[0][i] + if ensembl is None: + tcga.append(None) + continue + ensembl = ensembl.split("&")[0] + # Convert to Sequence Ontology controlled vocabulary + indel = x[1][i] + if indel == "DEL": + indel = "deletion" + if indel == "INS": + indel = "insertion" + ref = x[2][i].replace("-", "") + alt = x[3][i].replace("-", "") + inFrame = (abs(len(ref) - len(alt)) % 3) == 0 + + found = False + for (k, v) in variant_classes_all: + if ensembl == k: + tcga.append(v) + found = True + break + if found: + continue + + if indel == "deletion" and ( + ensembl == "frameshift_variant" + or (ensembl == "protein_altering_variant" and not inFrame) + ): + tcga.append("Frame_Shift_Del") + elif indel == "insertion" and ( + ensembl == "frameshift_variant" + or (ensembl == "protein_altering_variant" and not inFrame) + ): + tcga.append("Frame_Shift_Ins") + elif ensembl == "inframe_deletion" or ( + ensembl == "protein_altering_variant" and inFrame and indel == "deletion" + ): + tcga.append("In_Frame_Del") + elif ensembl == "inframe_insertion" or ( + ensembl == "protein_altering_variant" and inFrame and indel == "insertion" + ): + tcga.append("In_Frame_Ins") + else: + tcga.append("Targeted_Region") + + return tcga diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/vcf_to_table.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/vcf_to_table.py new file mode 100644 index 000000000..42034b3e0 --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/vcf_to_table.py @@ -0,0 +1,421 @@ +import argparse +import logging +from parser import VcfParser +import sys +import typing + +from action import Action +import exceptions +from functions import Functions +from ruamel.yaml import YAML +import vcfpy + + +def _get_command_line_parser(): + parser = argparse.ArgumentParser(description="VCF to MAF conversion") + + parser.add_argument("--config", help="configuration to parse the vcf file") + + parser.add_argument( + "--select-alt", + help="select one allele for output (generally set to 0), otherwise all alleles are output", + default=None, + type=int, + ) + parser.add_argument( + "--unique", + help="uniquify output (useful for repeated missing annotations)", + action="store_true", + ) + + parser.add_argument("--vcf-tumor-id", help="Tumor sample id as in the vcf column name") + parser.add_argument("--vcf-normal-id", help="Normal sample id as in the vcf column name") + parser.add_argument("--tumor-id", help="Tumor sample id output in the maf file") + parser.add_argument("--normal-id", help="Normal sample id output in the maf file") + + parser.add_argument( + "--NCBI_Build", help="Genome version (GRCh37 & GRCh38 are accepted by cBioPortal)" + ) + parser.add_argument("--Center", help="Name of the center for the MAF") + + parser.add_argument("--title", action="store_true", help="Write column names on output") + + parser.add_argument("--debug", action="store_true", help="Turn on debugging logs") + + parser.add_argument("vcf", help="Input vcf filename", nargs="?", default=None, type=str) + parser.add_argument( + "maf", help="Output maf file", nargs="?", type=argparse.FileType("w"), default=sys.stdout + ) + + return parser + + +def _check_config(config: typing.Dict[str, typing.Any]) -> typing.Dict[str, typing.Any]: + assert isinstance(config, dict), "Illegal (or empty) configuration file" + assert "output" in config, '"output" missing from configuration file' + assert isinstance(config["output"], dict), "Illegal (or empty) output definition" + for k, v in config["output"].items(): + assert isinstance(v, dict), 'Illegal (or empty) definition of output column "{}"'.format(k) + assert "input" in v or not isinstance( + v["input"], list + ), 'Missing inputs for output column "{}"'.format(k) + for i in range(len(v["input"])): + x = v["input"][i] + assert isinstance( + x, dict + ), "Illegal (or empty) element {} of inputs definition for output column {}".format( + i + 1, k + ) + assert ( + "set" in x and "column" in x + ), '"set" and/or "column" definition missing from element {} of inputs definition for output column {}'.format( + i + 1, k + ) + assert x["set"] in ( + "annotation", + "constant", + "fixed", + "format", + "info", + "variant", + ), 'Illegal set "{}" for input column "{}" of inputs definition for output column {}, must be one of "annotation", "constant", "fixed", "format", "info" or "variant"'.format( + x["set"], x["column"], k + ) + if x["set"] == "format": + assert ( + "sample" in x + ), 'Sample definition is missing from set "{}" for input column "{}" of inputs definition for output column {}, must be present for "format" sets'.format( + x["set"], x["column"], k + ) + if "on_missing" in x: + assert x["on_missing"] in ( + "stop", + "skip", + "default", + "ignore", + ), 'Illegal value of requested action for missing input "{}" for output column "{}", must be either "stop", "skip", "default" or "ignore"'.format( + x["column"], k + ) + else: + config["output"][k]["input"][i]["on_missing"] = "ignore" + if x["on_missing"] == "default": + assert ( + "default" in x and x["default"] is not None + ), 'Missing default value for input "{}" for output column "{}"'.format( + x["column"], k + ) + else: + config["output"][k]["input"][i]["default"] = None + if "on_missing" in v: + assert v["on_missing"] in ( + "stop", + "skip", + "default", + "ignore", + ), 'Illegal value of requested action for output column "{}", must be either "stop", "skip", "default" or "ignore"'.format( + k + ) + else: + config["output"][k]["on_missing"] = "ignore" + if v["on_missing"] == "default": + assert ( + "default" in v and v["default"] is not None + ), 'Missing default value for output column "{}"'.format(k) + else: + config["output"][k]["default"] = None + return config + + +def _add_constants(parser: VcfParser, args): + constants = ("NCBI_Build", "Center") + for constant in constants: + parser.addConstant(constant, vars(args).get(constant, None)) + parser.addConstant("tumor_id", args.tumor_id if args.tumor_id else args.vcf_tumor_id) + parser.addConstant("normal_id", args.normal_id if args.normal_id else args.vcf_normal_id) + + +def _get_column_values(record, parser, description, functions): + arguments = [] + for i in range(len(description["input"])): + inputs = description["input"][i] + value = parser.getInputValue( + record=record, + theSet=inputs["set"], + theColumn=inputs["column"], + theSample=inputs.get("sample", None), + default=inputs.get("default", None), + ) + + if description.get("action", "ignore") == "stop": + if value is None: + raise exceptions.ActionStop( + 'Missing mandatory input "{}" of set "{}"'.format( + inputs["column"], inputs["set"] + ) + ) + for alt in record.ALT: + if alt.value not in value or value[alt.value] is None: + raise exceptions.ActionStop( + 'Missing mandatory input "{}" of set "{}" for alt variant "{}"'.format( + inputs["column"], inputs["set"], alt.value + ) + ) + for i in range(len(value[alt.value])): + if value[alt.value][i] is None: + raise exceptions.ActionStop( + 'Missing mandatory element {} from input "{}" of set "{}" for alt variant "{}"'.format( + i + 1, inputs["column"], inputs["set"], alt.value + ) + ) + + arguments.append(value) + return functions.run( + arguments, + description.get("function", "identity"), + description.get("args", None), + description.get("default", None), + ) + + +def _check_result( + result: typing.Dict[str, typing.List[typing.Any]], + action: str, + default: str, + alts: typing.List[str], +) -> typing.Dict[str, typing.List[typing.Any]]: + assert action != "default" or default is not None + + if result is None: + if action == "stop": + raise exceptions.ActionStop("Missing result") + elif action == "default": + result = {alt: [default] for alt in alts} + else: + pass + else: + assert isinstance(result, dict) + for alt in alts: + if alt not in result or result[alt] is None: + if action == "stop": + raise exceptions.ActionStop('Missing result for allele "{}"'.format(alt)) + elif action == "default": + result[alt] = [default] + else: + pass + else: + assert isinstance(result[alt], list) + for i in range(len(result[alt])): + if result[alt][i] is None: + if action == "stop": + raise exceptions.ActionStop( + 'Missing element {} from result for allele "{}"'.format(i + 1, alt) + ) + elif action == "default": + result[alt][i] = default + else: + pass + return result + + +def _update_one_status(status, result, action): + if status == Action.SKIP: + return status + assert isinstance(status, list) + + if result is None: + if action == "stop": + raise exceptions.ActionStopException("Missing value") + if action == "skip": + return Action.SKIP + return status + assert isinstance(result, list) + + if len(status) == 1 and len(result) > 1: + status = [status[0] for i in range(len(result))] + if len(status) > 1 and len(result) == 1: + result = [result[0] for i in range(len(status))] + if len(result) != len(status): + raise exceptions.IllegalValue( + "Expansion impossible, previous length = {}, current length = {}".format( + len(status), len(result) + ) + ) + + for i in range(len(result)): + if result[i] is not None: + continue + if action == "stop": + raise exceptions.ActionStopException("Missing value") + if action == "skip": + status[i] = Action.SKIP + return status + + +def _update_status(status, result, description): + if status == Action.SKIP: + return status + + if result is None: + if description.get("on_missing", "ignore") == "skip": + return Action.SKIP + else: + return status + assert isinstance(result, dict) + + for alt, s in status.items(): + status[alt] = _update_one_status( + s, result.get(alt, None), description.get("on_missing", "ignore") + ) + return status + + +def _add_to_output(results, status, alts, record): + if status != Action.SKIP: + assert isinstance(status, dict) + for alt in alts: + if status[alt] == Action.SKIP: + logging.info("Skipped record {}".format(vcf_record_to_string(record))) + continue + for i in range(len(status[alt])): + if status[alt][i] == Action.SKIP: + logging.info("Skipped record {}".format(vcf_record_to_string(record))) + continue + row = [] + for col, result in results.items(): + r = None + if alt in result and result[alt]: + assert isinstance(result[alt], list) + if len(result[alt]) == 1: + r = result[alt][0] + else: + r = result[alt][i] + row.append(r) + yield [str(x) if x is not None else "" for x in row] + else: + logging.info("Skipped record {}".format(vcf_record_to_string(record))) + + +def vcf_record_to_string(record): + fields = [ + record.CHROM, + str(record.POS), + record.REF, + ",".join([alt.value for alt in record.ALT]), + ] + info = list() + for k, v in record.INFO.items(): + if isinstance(v, list) and not isinstance(v, str): + v = ",".join([str(el) for el in v]) + info.append("{}={}".format(k, str(v))) + fields.append(";".join(info)) + for call in record.calls: + fmt = list() + for v in call.data.values(): + if isinstance(v, list) and not isinstance(v, str): + v = ",".join([str(el) for el in v]) + fmt.append(str(v)) + fields.append(";".join(fmt)) + return "\t".join(fields) + + +def main(): + parser = _get_command_line_parser() + args = parser.parse_args() + + logging.basicConfig( + format="%(asctime)s %(levelname)s: %(message)s", + level=logging.DEBUG if args.debug else logging.WARNING, + ) + + if not args.vcf_tumor_id and not args.vcf_normal_id: + logging.error("Missing tumor and normal vcf ids") + return -1 + samples = {"tumor": args.vcf_tumor_id, "normal": args.vcf_normal_id} + + with open(args.config, "r") as f: + logging.info("Loading configuration from {}".format(args.config)) + config = YAML().load(f) + try: + config = _check_config(config) + except AssertionError as e: + logging.error(e) + return -1 + + functions = Functions(config) + + if args.vcf is None: + logging.info("Reading VCF file from stdin") + reader = vcfpy.Reader.from_stream(sys.stdin) + else: + logging.info("Reading VCF file {}".format(args.vcf)) + reader = vcfpy.Reader.from_path(args.vcf) + vcf = VcfParser(config, reader.header, samples) + + _add_constants(vcf, args) + + if args.title: + print("\t".join(config["output"].keys()), file=args.maf) + + unique = set() + try: + iRecord = 0 + for record in reader: + iRecord += 1 + + if args.select_alt is not None: + if args.select_alt >= len(record.ALT): + logging.info( + "Record {} ignored, number of alt alleles ({}) smaller than requested ({})".format( + iRecord, len(record.ALT), args.select_alt + 1 + ) + ) + continue + record = vcf.subset(record, args.select_alt) + vcf.annotation.set_minimizer(record) + alts = [alt.value for alt in record.ALT] + + status = {alt: [Action.OK] for alt in alts} + results = {} + for column, description in config["output"].items(): + result = _get_column_values(record, vcf, description, functions) + + results[column] = _check_result( + result, + description.get("on_missing", "ignore"), + description.get("default", None), + alts, + ) + + status = _update_status(status, results[column], description) + if status == Action.SKIP: + logging.info("Skipped record {}".format(vcf_record_to_string(record))) + break + for row in _add_to_output(results, status, alts, record): + s = "\t".join(row) + if args.unique and s in unique: + continue + print(s, file=args.maf) + unique.add(s) + except exceptions.FunctionError as e: + logging.error( + 'Error during compution of values for column request "{}" of record {}:{}'.format( + column, record.CHROM, record.POS + ) + ) + logging.error("Message: {}".format(e)) + return -1 + except exceptions.ActionStop as e: + logging.error( + 'Missing mandatory value for column request "{}" of record {}:{}'.format( + column, record.CHROM, record.POS + ) + ) + logging.error("Message: {}".format(e)) + return -1 + + logging.info("Conversion complete, processed {} VCF records".format(iRecord)) + return 0 + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py new file mode 100644 index 000000000..d48c77bae --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py @@ -0,0 +1,57 @@ +# -*- coding: utf-8 -*- +"""Wrapper for running VCF2MAF incl VEP variant annotation +""" + +import os + +from snakemake.shell import shell + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step] + +vcf_to_table = os.path.join(os.path.dirname(os.path.realpath(__file__)), "vcf_to_table.py") +vcf_to_table_config = os.path.join(os.path.dirname(os.path.realpath(__file__)), "config.yaml") + +params = snakemake.params.args + +shell( + r""" +set -x + +# Also pipe everything to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec &> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +python {vcf_to_table} \ + --config {vcf_to_table_config} \ + --debug --unique --title \ + --NCBI_Build {config[vcf2maf][ncbi_build]} --Center {config[vcf2maf][Center]} \ + --vcf-tumor-id {params[tumor_sample]} --tumor-id {params[tumor_id]} \ + --vcf-normal-id {params[normal_sample]} --normal-id {params[normal_id]} \ + {snakemake.input.vcf} {snakemake.output.maf} + +pushd $(dirname {snakemake.output.maf}) +md5sum $(basename {snakemake.output.maf}) > $(basename {snakemake.output.maf}).md5 +popd +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py b/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py index 780a8d6de..965c5e758 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py +++ b/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py @@ -1,7 +1,6 @@ # -*- coding: utf-8 -*- """Tests for the cbioportal_export workflow module code""" -from pathlib import Path import textwrap import pytest @@ -10,35 +9,10 @@ from snappy_pipeline.workflows.cbioportal_export import cbioportalExportWorkflow +from .common import get_expected_log_files_dict from .conftest import patch_module_fs -@pytest.fixture -def cbioportal_zscores_get_df_content(): - """Return contents of Z-Score data frame.""" - p1 = "P001-T1" - p2 = "P002-T2" - som_base = ( - "SOM_CNV_CALLING/output/bwa.copywriter.{p}-DNA1-WGS1/out/" - "bwa.copywriter.{p}-DNA1-WGS1_gene_call.txt" - ) - gexp_base = ( - "GENE_EXP_QUANTIFICATION/output/star.featurecounts.{p}-RNA1-mRNA_seq1/out/" - "star.featurecounts.{p}-RNA1-mRNA_seq1.tsv" - ) - p1_som = som_base.format(p=p1) - p1_gexp = gexp_base.format(p=p1) - p2_som = som_base.format(p=p2) - p2_gexp = gexp_base.format(p=p2) - return textwrap.dedent( - f""" - ID\tgene_call_filename\tcount_filename - {p1}\t{p1_som}\t{p1_gexp} - {p2}\t{p2_som}\t{p2_gexp} - """ - ).lstrip() - - @pytest.fixture(scope="module") # otherwise: performance issues def minimal_config(): """Return YAML parsing result for configuration""" @@ -50,30 +24,28 @@ def minimal_config(): reference: path: /path/to/ref.fa - cbioportal_export: - # Paths to snappy steps containing results to be uploaded - path_ngs_mapping: /NGS_MAPPING - path_gene_expression_quantification: /GENE_EXP_QUANTIFICATION - path_somatic_variant_filtration: /SOM_VAR_FILTRATION - path_copy_number_step: /SOM_CNV_CALLING - # Select tools & filter set - cnv_tool: control_freec - tools_somatic_variant_calling: [ "mutect2" ] - filter_set: dkfz_and_ebfilter - exclude_variant_with_flag: LowFisherScore - # Additional parameters - vep_data_path: /path/to/VEP/static_data/GRCh37 - species: homo_sapiens - # ncbi_build: GRCh37 - filter_vcf: /path/to/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz - cache_version: 100 - vep_custom: "" - # Description of dataset in cBioPortal - type_of_cancer: mixed - cancer_study_id: mixed_pedion_a02p - study_description: "PeDiOn project A02P" - study_name: PeDiOn_A02P - study_name_short: A02P + step_config: + ngs_mapping: + star: + path_features: /path/to/gtf + cbioportal_export: + # Paths to snappy steps containing results to be uploaded + path_ngs_mapping: /NGS_MAPPING + expression_tool: star + path_somatic_variant: /SOM_VAR_FILTRATION + somatic_variant_calling_tool: mutect2 + somatic_variant_annotation_tool: "vep" + filter_set: dkfz_only + path_copy_number: /COPY_NUMBER + copy_number_tool: cnvkit + exclude_variant_with_flag: LowFisherScore + # Description of dataset in cBioPortal + study: + type_of_cancer: mixed + cancer_study_id: mixed_pedion_a02p + study_description: "PeDiOn project A02P" + study_name: PeDiOn_A02P + study_name_short: A02P data_sets: first_batch: @@ -102,10 +74,9 @@ def cbioportal_export_workflow( # Patch out file-system related things in abstract (the crawling link in step is defined there) patch_module_fs("snappy_pipeline.workflows.abstract", cancer_sheet_fake_fs, mocker) dummy_workflow.globals = { - "ngs_mapping": lambda x: "NGS_MAPPING/" + x, - "copy_number_step": lambda x: "SOM_CNV_CALLING/" + x, - "somatic_variant_filtration": lambda x: "SOM_VAR_FILTRATION/" + x[0], - "gene_expression_quantification": lambda x: "GENE_EXP_QUANTIFICATION/" + x, + "ngs_mapping": lambda x: "/NGS_MAPPING/" + x, + "somatic_variant": lambda x: "/SOM_VAR_FILTRATION/" + x, + "copy_number_step": lambda x: "/COPY_NUMBER/" + x, } # Construct the workflow object return cbioportalExportWorkflow( @@ -117,65 +88,33 @@ def cbioportal_export_workflow( ) -# Tests for CbioportalStudyMetaFilesStepPart ----------------------------------------------------- - - -def test_cbioportal_study_meta_files_step_part_get_input_files(cbioportal_export_workflow): - """Tests CbioportalStudyMetaFilesStepPart.get_input_files()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_output_files("cbioportal_study_meta_files", "run") - - -def test_cbioportal_study_meta_files_step_part_get_output_files(cbioportal_export_workflow): - """Tests CbioportalStudyMetaFilesStepPart.get_output_files()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_output_files("cbioportal_study_meta_files", "run") - - -def test_cbioportal_study_meta_files_step_part_get_log_file(cbioportal_export_workflow): - """Tests CbioportalStudyMetaFilesStepPart.get_log_file()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_log_file("cbioportal_study_meta_files", "run") - - -def test_cbioportal_study_meta_files_step_part_get_resource_usage(cbioportal_export_workflow): - """Tests CbioportalStudyMetaFilesStepPart.get_resource_usage()""" - # Define expected: default defined workflow.abstract - expected_dict = {"threads": 1, "time": "01:00:00", "memory": "2G", "partition": "medium"} - # Evaluate - for resource, expected in expected_dict.items(): - msg_error = f"Assertion error for resource '{resource}'." - actual = cbioportal_export_workflow.get_resource( - "cbioportal_study_meta_files", "run", resource - ) - assert actual == expected, msg_error - - -# Tests for cbioportalMetaFilesStepPart ------------------------------------------------------------ +# Tests for cbioportalMetaFilesStepPart ----------------------------------------------------- def test_cbioportal_meta_files_step_part_get_input_files(cbioportal_export_workflow): """Tests cbioportalMetaFilesStepPart.get_input_files()""" # Method not implemented with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_input_files("cbioportal_meta_files", "run")(None) + cbioportal_export_workflow.get_input_files("cbioportal_meta_files", "run") def test_cbioportal_meta_files_step_part_get_output_files(cbioportal_export_workflow): - """Tests cbioportalMetaFilesStepPart.get_output_files()""" + """Tests CbioportalStudyMetaFilesStepPart.get_log_file()""" + # Define expected: all meta files as somatic variants, CNA, segmentation & expression are present expected = [ - "work/upload/meta_clinical_patient.txt", - "work/upload/meta_clinical_sample.txt", - "work/upload/meta_CNA_gistic.txt", - "work/upload/meta_CNA_log2.txt", - "work/upload/meta_expression_zscores.txt", - "work/upload/meta_mutation_extended.txt", - "work/upload/meta_segment.txt", + "work/upload/meta_{}.txt".format(x) + for x in ( + "study", + "clinical_patient", + "clinical_sample", + "mutation_extended", + "cna_gistic", + "cna_log2", + "segment", + "expression", + ) ] - actual = cbioportal_export_workflow.get_output_files("cbioportal_meta_files", "run") + actual = list(cbioportal_export_workflow.get_output_files("cbioportal_meta_files", "run")) assert actual == expected @@ -187,7 +126,7 @@ def test_cbioportal_meta_files_step_part_get_log_file(cbioportal_export_workflow def test_cbioportal_meta_files_step_part_get_resource_usage(cbioportal_export_workflow): - """Tests ExpansionHunterStepPart.get_resource_usage()""" + """Tests cbioportalMetaFilesStepPart.get_resource_usage()""" # Define expected: default defined workflow.abstract expected_dict = {"threads": 1, "time": "01:00:00", "memory": "2G", "partition": "medium"} # Evaluate @@ -203,16 +142,16 @@ def test_cbioportal_meta_files_step_part_get_resource_usage(cbioportal_export_wo def test_cbioportal_clinical_data_step_part_get_input_files(cbioportal_export_workflow): """Tests cbioportalClinicalDataStepPart.get_input_files()""" # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_input_files("cbioportal_clinical_data", "run")(None) + with pytest.raises(AssertionError): + cbioportal_export_workflow.get_input_files("cbioportal_clinical_data", "run") def test_cbioportal_clinical_data_step_part_get_output_files(cbioportal_export_workflow): """Tests cbioportalClinicalDataStepPart.get_output_files()""" # Define expected expected = { - "patients_tsv": "work/upload/data_clinical_patients.txt", - "samples_tsv": "work/upload/data_clinical_samples.txt", + "patient": "work/upload/data_clinical_patient.txt", + "sample": "work/upload/data_clinical_sample.txt", } # Get actual actual = cbioportal_export_workflow.get_output_files("cbioportal_clinical_data", "run") @@ -221,9 +160,12 @@ def test_cbioportal_clinical_data_step_part_get_output_files(cbioportal_export_w def test_cbioportal_clinical_data_step_part_get_log_file(cbioportal_export_workflow): """Tests cbioportalClinicalDataStepPart.get_log_file()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_log_file("cbioportal_clinical_data", "run") + # Define expected + base_name_out = "work/log/cbioportal_clinical_data" + expected = get_expected_log_files_dict(base_out=base_name_out, extended=False) + # Get actual + actual = cbioportal_export_workflow.get_log_file("cbioportal_clinical_data", "run") + assert actual == expected def test_cbioportal_clinical_data_step_part_get_resource_usage(cbioportal_export_workflow): @@ -239,30 +181,53 @@ def test_cbioportal_clinical_data_step_part_get_resource_usage(cbioportal_export assert actual == expected, msg_error +def test_cbioportal_clinical_data_step_part_get_args(cbioportal_export_workflow): + """Tests cbioportalClinicalDataStepPart.get_args()""" + # Define expected: all patients & samples + expected = { + "P001": {"P001-T1": {"DNA": "P001-T1-DNA1-WGS1", "RNA": "P001-T1-RNA1-mRNA_seq1"}}, + "P002": { + "P002-T1": {"DNA": "P002-T1-DNA1-WGS1"}, + "P002-T2": {"DNA": "P002-T2-DNA1-WGS1", "RNA": "P002-T2-RNA1-mRNA_seq1"}, + }, + } + actual = cbioportal_export_workflow.get_args("cbioportal_clinical_data", "run") + assert actual == expected + + # Tests for cbioportalCaseListsStepPart ---------------------------------------------------------- def test_cbioportal_case_lists_step_part_get_input_files(cbioportal_export_workflow): """Tests cbioportalCaseListsStepPart.get_input_files()""" # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_input_files("cbioportal_case_lists", "run")(None) + with pytest.raises(AssertionError): + cbioportal_export_workflow.get_input_files("cbioportal_case_lists", "run") def test_cbioportal_case_lists_step_part_get_output_files(cbioportal_export_workflow): """Tests cbioportalCaseListsStepPart.get_output_files()""" # Define expected - expected = {"sequenced": "work/upload/case_lists/all_cases_with_mutation_data.txt"} + expected = { + "sequenced": "work/upload/case_lists/all_cases_with_mutation_data.txt", + "cna": "work/upload/case_lists/all_cases_with_cna_data.txt", + "rna_seq_mrna": "work/upload/case_lists/all_cases_with_mrna_rnaseq_data.txt", + "cnaseq": "work/upload/case_lists/all_cases_with_mutation_and_cna_data.txt", + "3way_complete": "work/upload/case_lists/all_cases_with_mutation_and_cna_and_mrna_data.txt", + } # Get actual actual = cbioportal_export_workflow.get_output_files("cbioportal_case_lists", "run") assert actual == expected -def test_cbioportal_case_lists_step_part_get_log_file(cbioportal_export_workflow): +def test_cbioportal_case_lists_data_step_part_get_log_file(cbioportal_export_workflow): """Tests cbioportalCaseListsStepPart.get_log_file()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_log_file("cbioportal_case_lists", "run") + # Define expected + base_name_out = "work/log/cbioportal_case_lists" + expected = get_expected_log_files_dict(base_out=base_name_out, extended=False) + # Get actual + actual = cbioportal_export_workflow.get_log_file("cbioportal_case_lists", "run") + assert actual == expected def test_cbioportal_case_lists_step_part_get_resource_usage(cbioportal_export_workflow): @@ -276,6 +241,55 @@ def test_cbioportal_case_lists_step_part_get_resource_usage(cbioportal_export_wo assert actual == expected, msg_error +def test_cbioportal_case_lists_step_part_get_args(cbioportal_export_workflow): + """Tests cbioportalCaseListsStepPart.get_args()""" + # Define expected: all patients & samples + expected = { + "sequenced": { + "filename": "all_cases_with_mutation_data.txt", + "name": "Sequenced tumors", + "description": "Tumors with somatic variant calls", + "stable_id": "sequenced", + "category": "all_cases_with_mutation_data", + "samples": ["P001-T1", "P002-T1", "P002-T2"], + }, + "cna": { + "filename": "all_cases_with_cna_data.txt", + "name": "Tumors with CNA data", + "description": "Tumors with somatic Copy Number Alteration calls", + "stable_id": "cna", + "category": "all_cases_with_cna_data", + "samples": ["P001-T1", "P002-T1", "P002-T2"], + }, + "rna_seq_mrna": { + "filename": "all_cases_with_mrna_rnaseq_data.txt", + "name": "Tumors with expression data", + "description": "Tumors with mRNA seq expression data", + "stable_id": "rna_seq_mrna", + "category": "all_cases_with_mrna_rnaseq_data", + "samples": ["P001-T1", "P002-T2"], + }, + "cnaseq": { + "filename": "all_cases_with_mutation_and_cna_data.txt", + "name": "Sequenced tumors with CNA", + "description": "Tumors with somatic variant & CNA calls", + "stable_id": "cnaseq", + "category": "all_cases_with_mutation_and_cna_data", + "samples": ["P001-T1", "P002-T1", "P002-T2"], + }, + "3way_complete": { + "filename": "all_cases_with_mutation_and_cna_and_mrna_data.txt", + "name": "Sequenced tumors with CNA & expression", + "description": "Tumors with somatic variant calls, CNA calls & expression data", + "stable_id": "3way_complete", + "category": "all_cases_with_mutation_and_cna_and_mrna_data", + "samples": ["P001-T1", "P002-T2"], + }, + } + actual = cbioportal_export_workflow.get_args("cbioportal_case_lists", "run") + assert actual == expected + + # Tests for cbioportalVcf2MafStepPart ---------------------------------------------------------- @@ -283,9 +297,9 @@ def test_cbioportal_vcf2maf_step_part_get_input_files(cbioportal_export_workflow """Tests cbioportalVcf2MafStepPart.get_input_files()""" expected = { "vcf": ( - "SOM_VAR_FILTRATION/output/{mapper}.{caller}.jannovar_annotate_somatic_vcf." + "/SOM_VAR_FILTRATION/output/{mapper}.{caller}.{annotator}." "dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}.{exon_list}/out/" - "{mapper}.{caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." + "{mapper}.{caller}.{annotator}.dkfz_bias_filter.eb_filter." "{tumor_library}.{filter_set}.{exon_list}.vcf.gz" ) } @@ -298,9 +312,9 @@ def test_cbioportal_vcf2maf_step_part_get_output_files(cbioportal_export_workflo # Define expected expected = { "maf": ( - "work/maf/{mapper}.{caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." + "work/maf/{mapper}.{caller}.{annotator}.dkfz_bias_filter.eb_filter." "{tumor_library}.{filter_set}.{exon_list}/out/{mapper}.{caller}." - "jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." + "{annotator}.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." "{exon_list}.maf" ) } @@ -311,9 +325,17 @@ def test_cbioportal_vcf2maf_step_part_get_output_files(cbioportal_export_workflo def test_cbioportal_vcf2maf_step_part_get_log_file(cbioportal_export_workflow): """Tests cbioportalVcf2MafStepPart.get_log_file()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_log_file("cbioportal_vcf2maf", "run") + # Define expected + base_name_out = ( + "work/maf/{mapper}.{caller}.{annotator}.dkfz_bias_filter.eb_filter." + "{tumor_library}.{filter_set}.{exon_list}/log/{mapper}.{caller}." + "{annotator}.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." + "{exon_list}" + ) + expected = get_expected_log_files_dict(base_out=base_name_out, extended=False) + # Get actual + actual = cbioportal_export_workflow.get_log_file("cbioportal_vcf2maf", "run") + assert actual == expected def test_cbioportal_vcf2maf_step_part_get_args(cbioportal_export_workflow): @@ -332,7 +354,7 @@ def test_cbioportal_vcf2maf_step_part_get_args(cbioportal_export_workflow): def test_cbioportal_vcf2maf_step_part_get_resource_usage(cbioportal_export_workflow): """Tests cbioportalVcf2MafStepPart.get_resource_usage()""" # Define expected: default defined workflow.abstract - expected_dict = {"threads": 4, "time": "12:00:00", "memory": "5120M", "partition": "medium"} + expected_dict = {"threads": 2, "time": "02:00:00", "memory": "5120M", "partition": "medium"} # Evaluate for resource, expected in expected_dict.items(): msg_error = f"Assertion error for resource '{resource}'." @@ -340,219 +362,304 @@ def test_cbioportal_vcf2maf_step_part_get_resource_usage(cbioportal_export_workf assert actual == expected, msg_error -# Tests for cbioportalMafStepPart ---------------------------------------------------------------- +# Tests for cbioportalMutationsStepPart ---------------------------------------------------------------- -def test_cbioportal_maf_step_part_get_input_files(cbioportal_export_workflow): - """Tests cbioportalMafStepPart.get_input_files()""" +def test_cbioportal_mutations_step_part_get_input_files(cbioportal_export_workflow): + """Tests cbioportalMutationsStepPart.get_input_files()""" + sample = "P00{i}-T{t}" base_name = ( - "work/maf/bwa.mutect.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." + "work/maf/bwa.mutect2.vep.dkfz_bias_filter.eb_filter." "P00{i}-T{t}-DNA1-WGS1.dkfz_only.genome_wide/out/" - "bwa.mutect.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." + "bwa.mutect2.vep.dkfz_bias_filter.eb_filter." "P00{i}-T{t}-DNA1-WGS1.dkfz_only.genome_wide.maf" ) - expected = [base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2))] - actual = cbioportal_export_workflow.get_input_files("cbioportal_maf", "run") + expected = { + sample.format(i=i, t=t): base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2)) + } + actual = cbioportal_export_workflow.get_input_files("cbioportal_mutations", "run") assert actual == expected -def test_cbioportal_maf_step_part_get_output_files(cbioportal_export_workflow): - """Tests cbioportalMafStepPart.get_output_files()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_output_files("cbioportal_maf", "run") +def test_cbioportal_mutations_step_part_get_output_files(cbioportal_export_workflow): + """Tests cbioportalMutationsStepPart.get_output_files()""" + # Define expected: default defined workflow.abstract + expected = "work/upload/data_mutation_extended.txt" + # Actual + actual = cbioportal_export_workflow.get_output_files("cbioportal_mutations", "run") + assert actual == expected -def test_cbioportal_maf_step_part_get_log_file(cbioportal_export_workflow): - """Tests cbioportalMafStepPart.get_log_file()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_log_file("cbioportal_maf", "run") +def test_cbioportal_mutations_step_part_get_log_file(cbioportal_export_workflow): + """Tests cbioportalMutationsStepPart.get_log_file()""" + # Define expected + base_name_out = "work/log/cbioportal_mutations" + expected = get_expected_log_files_dict(base_out=base_name_out, extended=False) + # Get actual + actual = cbioportal_export_workflow.get_log_file("cbioportal_mutations", "run") + assert actual == expected -def test_cbioportal_maf_step_part_get_resource_usage(cbioportal_export_workflow): - """Tests cbioportalMafStepPart.get_resource_usage()""" +def test_cbioportal_mutations_step_part_get_resource_usage(cbioportal_export_workflow): + """Tests cbioportalMutationsStepPart.get_resource_usage()""" # Define expected: default defined workflow.abstract expected_dict = {"threads": 1, "time": "01:00:00", "memory": "2G", "partition": "medium"} # Evaluate for resource, expected in expected_dict.items(): msg_error = f"Assertion error for resource '{resource}'." - actual = cbioportal_export_workflow.get_resource("cbioportal_maf", "run", resource) + actual = cbioportal_export_workflow.get_resource("cbioportal_mutations", "run", resource) + assert actual == expected, msg_error + + +# Tests for cbioportalCns2CnaStepPart ----------------------------------------------------------- + + +def test_cbioportal_cns2cna_step_part_get_input_files(cbioportal_export_workflow): + """Tests cbioportalCns2CnaStepPart.get_input_files()""" + expected = { + "cns": "/COPY_NUMBER/output/{mapper}.{caller}.{tumor_library}/out/{mapper}.{caller}.{tumor_library}.cns" + } + actual = cbioportal_export_workflow.get_input_files("cbioportal_cns2cna", "run") + assert actual == expected + + +def test_cbioportal_cns2cna_step_part_get_output_files(cbioportal_export_workflow): + """Tests cbioportalCns2CnaStepPart.get_output_files()""" + # Define expected + expected = { + "cna": "work/cna/{mapper}.{caller}.{tumor_library}/out/{mapper}.{caller}.{tumor_library}.cna" + } + # Get actual + actual = cbioportal_export_workflow.get_output_files("cbioportal_cns2cna", "run") + assert actual == expected + + +def test_cbioportal_cns2cna_step_part_get_log_file(cbioportal_export_workflow): + """Tests cbioportalCns2CnaStepPart.get_log_file()""" + # Define expected + base_name_out = ( + "work/cna/{mapper}.{caller}.{tumor_library}/log/{mapper}.{caller}.{tumor_library}" + ) + expected = get_expected_log_files_dict(base_out=base_name_out, extended=False) + # Get actual + actual = cbioportal_export_workflow.get_log_file("cbioportal_cns2cna", "run") + assert actual == expected + + +def test_cbioportal_cns2cna_step_part_get_args(cbioportal_export_workflow): + """Tests cbioportalCns2CnaStepPart.get_args()""" + expected = { + "features": "/path/to/gtf", + "pipeline_id": "ENSEMBL", + } + actual = cbioportal_export_workflow.get_args("cbioportal_cns2cna", "run") + assert actual == expected + + +def test_cbioportal_cns2cna_step_part_get_resource_usage(cbioportal_export_workflow): + """Tests cbioportalCns2CnaStepPart.get_resource_usage()""" + # Define expected: default defined workflow.abstract + expected_dict = {"threads": 2, "time": "02:00:00", "memory": "8192M", "partition": "medium"} + # Evaluate + for resource, expected in expected_dict.items(): + msg_error = f"Assertion error for resource '{resource}'." + actual = cbioportal_export_workflow.get_resource("cbioportal_cns2cna", "run", resource) assert actual == expected, msg_error # Tests for cbioportalCnaFilesStepPart ----------------------------------------------------------- -def test_cbioportal_cna_data_step_part_get_input_files_log2(cbioportal_export_workflow): +def test_cbioportal_cna_step_part_get_input_files_log2(cbioportal_export_workflow): """Tests cbioportalCnaFilesStepPart.get_input_files() - action 'log2'""" # Define expected - base_name = ( - "SOM_CNV_CALLING/output/bwa.copywriter.P00{i}-T{t}-DNA1-WGS1/out/" - "bwa.copywriter.P00{i}-T{t}-DNA1-WGS1_gene_log2.txt" - ) - expected = [base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2))] + sample = "P00{i}-T{t}" + base_name = "work/cna/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/out/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.cna" + expected = { + sample.format(i=i, t=t): base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2)) + } # Get actual - actual = cbioportal_export_workflow.get_input_files("cbioportal_cna_data", "log2") + actual = cbioportal_export_workflow.get_input_files("cbioportal_cna", "log2") assert actual == expected -def test_cbioportal_cna_data_step_part_get_input_files_gistic(cbioportal_export_workflow): +def test_cbioportal_cna_step_part_get_input_files_gistic(cbioportal_export_workflow): """Tests cbioportalCnaFilesStepPart.get_input_files() - action 'gistic'""" # Define expected - base_name = ( - "SOM_CNV_CALLING/output/bwa.copywriter.P00{i}-T{t}-DNA1-WGS1/out/" - "bwa.copywriter.P00{i}-T{t}-DNA1-WGS1_gene_call.txt" - ) - expected = [base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2))] + sample = "P00{i}-T{t}" + base_name = "work/cna/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/out/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.cna" + expected = { + sample.format(i=i, t=t): base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2)) + } # Get actual - actual = cbioportal_export_workflow.get_input_files("cbioportal_cna_data", "gistic") + actual = cbioportal_export_workflow.get_input_files("cbioportal_cna", "gistic") assert actual == expected -def test_cbioportal_cna_data_step_part_get_input_files_segments(cbioportal_export_workflow): - """Tests cbioportalCnaFilesStepPart.get_input_files() - action 'segments'""" +def test_cbioportal_cna_step_part_get_output_files_log2(cbioportal_export_workflow): + """Tests cbioportalCnaFilesStepPart.get_output_files() - action 'log2'""" # Define expected - base_name = ( - "SOM_CNV_CALLING/output/bwa.copywriter.P00{i}-T{t}-DNA1-WGS1/out/" - "bwa.copywriter.P00{i}-T{t}-DNA1-WGS1_segments.txt" - ) - expected = [base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2))] + expected = "work/upload/data_cna_log2.txt" # Get actual - actual = cbioportal_export_workflow.get_input_files("cbioportal_cna_data", "segments") + actual = cbioportal_export_workflow.get_output_files("cbioportal_cna", "log2") assert actual == expected -def test_cbioportal_cna_data_step_part_get_output_files(cbioportal_export_workflow): - """Tests cbioportalCnaFilesStepPart.get_output_files()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_output_files("cbioportal_cna_data", "action") +def test_cbioportal_cna_step_part_get_output_files_gistic(cbioportal_export_workflow): + """Tests cbioportalCnaFilesStepPart.get_output_files() - action 'gistic'""" + # Define expected + expected = "work/upload/data_cna_gistic.txt" + # Get actual + actual = cbioportal_export_workflow.get_output_files("cbioportal_cna", "gistic") + assert actual == expected -def test_cbioportal_cna_data_step_part_get_log_file(cbioportal_export_workflow): +def test_cbioportal_cna_step_part_get_log_file(cbioportal_export_workflow): """Tests cbioportalCnaFilesStepPart.get_log_file()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_log_file("cbioportal_cna_data", "action") + # Define expected + base_name_out = "work/log/cbioportal_cna" + expected = get_expected_log_files_dict(base_out=base_name_out, extended=False) + # Get actual + actual = cbioportal_export_workflow.get_log_file("cbioportal_cna", "log2") + assert actual == expected + + +def test_cbioportal_cna_step_part_get_args_log2(cbioportal_export_workflow): + """Tests cbioportalCnaFilesStepPart.get_args() -action 'log2'""" + # Define expected + base_name_out = "work/log/cbioportal_cna" + expected = { + "action_type": "log2", + "extra_args": {"amplification": "9", "pipeline_id": "ENSEMBL"}, + } + # Get actual + actual = cbioportal_export_workflow.get_args("cbioportal_cna", "log2") + assert actual == expected + +def test_cbioportal_cna_step_part_get_args_gistic(cbioportal_export_workflow): + """Tests cbioportalCnaFilesStepPart.get_args() -action 'gistic'""" + # Define expected + base_name_out = "work/log/cbioportal_cna" + expected = {"action_type": "gistic", "extra_args": {"pipeline_id": "ENSEMBL"}} + # Get actual + actual = cbioportal_export_workflow.get_args("cbioportal_cna", "gistic") + assert actual == expected -def test_cbioportal_cna_data_step_part_get_resource_usage(cbioportal_export_workflow): + +def test_cbioportal_cna_step_part_get_resource_usage(cbioportal_export_workflow): """Tests cbioportalCnaFilesStepPart.get_resource_usage()""" # Define expected - expected_dict = {"threads": 2, "time": "01:00:00", "memory": "8G", "partition": "medium"} + expected_dict = {"threads": 2, "time": "02:00:00", "memory": "8192M", "partition": "medium"} # Evaluate - all_actions = cbioportal_export_workflow.substep_getattr("cbioportal_cna_data", "actions") + all_actions = cbioportal_export_workflow.substep_getattr("cbioportal_cna", "actions") for action in all_actions: for resource, expected in expected_dict.items(): msg_error = f"Assertion error for resource '{resource}' in action '{action}'." - actual = cbioportal_export_workflow.get_resource( - "cbioportal_cna_data", action, resource - ) + actual = cbioportal_export_workflow.get_resource("cbioportal_cna", action, resource) assert actual == expected, msg_error -# Tests for cbioportalZscoresStepPart ------------------------------------------------------------ +# Tests for cbioportalSegmentStepPart -------------------------------------------------------- -def test_cbioportal_zscores_step_part_get_input_files(cbioportal_export_workflow): - """Tests cbioportalZscoresStepPart.get_input_files()""" +def test_cbioportal_segment_step_part_get_input_files(cbioportal_export_workflow): + """Tests cbioportalSegmentStepPart.get_input_files()""" # Define expected - p1 = "P001-T1" - p2 = "P002-T2" - som_base = ( - "SOM_CNV_CALLING/output/bwa.copywriter.{p}-DNA1-WGS1/out/" - "bwa.copywriter.{p}-DNA1-WGS1_gene_call.txt" - ) - gexp_base = ( - "GENE_EXP_QUANTIFICATION/output/star.featurecounts.{p}-RNA1-mRNA_seq1/out/" - "star.featurecounts.{p}-RNA1-mRNA_seq1.tsv" - ) - expected = [ - (p1, som_base.format(p=p1), gexp_base.format(p=p1)), - (p2, som_base.format(p=p2), gexp_base.format(p=p2)), - ] + sample = "P00{i}-T{t}" + base_name = "/COPY_NUMBER/output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/out/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.cns" + expected = { + sample.format(i=i, t=t): base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2)) + } # Get actual - actual = cbioportal_export_workflow.get_input_files("cbioportal_zscores", "get_zscores_input") - actual = sorted(actual) + actual = cbioportal_export_workflow.get_input_files("cbioportal_segment", "run") assert actual == expected -def test_cbioportal_zscores_step_part_get_output_files(cbioportal_export_workflow): - """Tests cbioportalZscoresStepPart.get_output_files()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_output_files("cbioportal_zscores", "run") - - -def test_cbioportal_zscores_step_part_get_log_file(cbioportal_export_workflow): - """Tests cbioportalZscoresStepPart.get_log_file()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_log_file("cbioportal_zscores", "run") +def test_cbioportal_segment_step_part_get_output_files(cbioportal_export_workflow): + """Tests cbioportalSegmentStepPart.get_output_files()""" + # Define expected + expected = "work/upload/data_segment.txt" + # Actual + actual = cbioportal_export_workflow.get_output_files("cbioportal_segment", "run") + assert actual == expected -def test_cbioportal_zscores_step_part_get_df( - cbioportal_export_workflow, cbioportal_zscores_get_df_content, tmpdir -): - """Tests cbioportalZscoresStepPart.get_df()""" +def test_cbioportal_segment_step_part_get_log_file(cbioportal_export_workflow): + """Tests cbioportalSegmentStepPart.get_log_file()""" # Define expected - expected = cbioportal_zscores_get_df_content - # Prepare method input in temporary directory - _tmp_work_dir = tmpdir.mkdir("work") - output_path = str(_tmp_work_dir.join("zscores_mapping_df.tsv")) - output = (output_path,) - # Get actual and assert - cbioportal_export_workflow.substep_getattr("cbioportal_zscores", "get_df")(output) - actual = Path(output_path).read_text(encoding="utf8") + base_name_out = "work/log/cbioportal_segment" + expected = get_expected_log_files_dict(base_out=base_name_out, extended=False) + # Get actual + actual = cbioportal_export_workflow.get_log_file("cbioportal_segment", "run") assert actual == expected -def test_cbioportal_zscores_step_part_get_resource_usage(cbioportal_export_workflow): - """Tests cbioportalZscoresStepPart.get_resource_usage()""" +def test_cbioportal_segment_step_part_get_resource_usage(cbioportal_export_workflow): + """Tests cbioportalSegmentStepPart.get_resource_usage()""" # Define expected: default defined workflow.abstract - expected_dict = {"threads": 1, "time": "01:00:00", "memory": "2G", "partition": "medium"} + expected_dict = {"threads": 2, "time": "02:00:00", "memory": "8192M", "partition": "medium"} # Evaluate for resource, expected in expected_dict.items(): msg_error = f"Assertion error for resource '{resource}'." - actual = cbioportal_export_workflow.get_resource("cbioportal_zscores", "run", resource) + actual = cbioportal_export_workflow.get_resource("cbioportal_segment", "run", resource) assert actual == expected, msg_error -# Tests for CbioportalComputeZscoresStepPart ----------------------------------------------------- +# Tests for cbioportalExpressionStepPart ----------------------------------------------------- -def test_cbioportal_compute_zscores_step_part_get_input_files(cbioportal_export_workflow): - """Tests CbioportalComputeZscoresStepPart.get_input_files()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_output_files("cbioportal_compute_zscores", "run") +def test_cbioportal_expression_step_part_get_input_files(cbioportal_export_workflow): + """Tests cbioportalExpressionStepPart.get_input_files()""" + # Define expected + sample = "P00{i}-T{t}" + base_name = ( + "/NGS_MAPPING/output/star.P00{i}-T{t}-RNA1-mRNA_seq1/out/" + "star.P00{i}-T{t}-RNA1-mRNA_seq1.GeneCounts.tab" + ) + expected = {sample.format(i=i, t=t): base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 2))} + # Get actual + actual = cbioportal_export_workflow.get_input_files("cbioportal_expression", "run") + assert actual == expected -def test_cbioportal_compute_zscores_step_part_get_output_files(cbioportal_export_workflow): - """Tests CbioportalComputeZscoresStepPart.get_output_files()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_output_files("cbioportal_compute_zscores", "run") +def test_cbioportal_expression_step_part_get_output_files(cbioportal_export_workflow): + """Tests cbioportalExpressionStepPart.get_output_files()""" + # Define expected + expected = "work/upload/data_expression.txt" + # Actual + actual = cbioportal_export_workflow.get_output_files("cbioportal_expression", "run") + assert actual == expected -def test_cbioportal_compute_zscores_step_part_get_log_file(cbioportal_export_workflow): - """Tests CbioportalComputeZscoresStepPart.get_log_file()""" - # Method not implemented - with pytest.raises(NotImplementedError): - cbioportal_export_workflow.get_log_file("cbioportal_compute_zscores", "run") +def test_cbioportal_expression_step_part_get_log_file(cbioportal_export_workflow): + """Tests cbioportalExpressionStepPart.get_log_file()""" + # Define expected + base_name_out = "work/log/cbioportal_expression" + expected = get_expected_log_files_dict(base_out=base_name_out, extended=False) + # Get actual + actual = cbioportal_export_workflow.get_log_file("cbioportal_expression", "run") + assert actual == expected + +def test_cbioportal_expression_step_part_get_args(cbioportal_export_workflow): + """Tests cbioportalExpressionStepPart.get_args()""" + expected = { + "action_type": "expression", + "extra_args": {"tx_obj": "/path/to/gtf", "pipeline_id": "ENSEMBL"}, + } + actual = cbioportal_export_workflow.get_args("cbioportal_expression", "run") + assert actual == expected -def test_cbioportal_compute_zscores_step_part_get_resource_usage(cbioportal_export_workflow): - """Tests CbioportalComputeZscoresStepPart.get_resource_usage()""" + +def test_cbioportal_expression_step_part_get_resource_usage(cbioportal_export_workflow): + """Tests cbioportalExpressionStepPart.get_resource_usage()""" # Define expected: default defined workflow.abstract - expected_dict = {"threads": 1, "time": "01:00:00", "memory": "2G", "partition": "medium"} + expected_dict = {"threads": 2, "time": "02:00:00", "memory": "8192M", "partition": "medium"} # Evaluate for resource, expected in expected_dict.items(): msg_error = f"Assertion error for resource '{resource}'." - actual = cbioportal_export_workflow.get_resource( - "cbioportal_compute_zscores", "run", resource - ) + actual = cbioportal_export_workflow.get_resource("cbioportal_expression", "run", resource) assert actual == expected, msg_error @@ -565,36 +672,41 @@ def test_cbioportal_export_workflow(cbioportal_export_workflow): expected = [ "cbioportal_case_lists", "cbioportal_clinical_data", - "cbioportal_cna_data", - "cbioportal_compute_zscores", - "cbioportal_maf", + "cbioportal_cna", + "cbioportal_cns2cna", + "cbioportal_expression", "cbioportal_meta_files", - "cbioportal_study_meta_files", + "cbioportal_mutations", + "cbioportal_segment", "cbioportal_vcf2maf", - "cbioportal_zscores", - "link_out", ] actual = list(sorted(cbioportal_export_workflow.sub_steps.keys())) assert actual == expected # Check result file construction expected = [ + "work/upload/case_lists/all_cases_with_cna_data.txt", + "work/upload/case_lists/all_cases_with_mrna_rnaseq_data.txt", + "work/upload/case_lists/all_cases_with_mutation_and_cna_and_mrna_data.txt", + "work/upload/case_lists/all_cases_with_mutation_and_cna_data.txt", "work/upload/case_lists/all_cases_with_mutation_data.txt", - "work/upload/data_CNA_gistic.txt", - "work/upload/data_CNA_log2.txt", - "work/upload/data_clinical_patients.txt", - "work/upload/data_clinical_samples.txt", - "work/upload/data_expression_zscores.txt", + "work/upload/data_clinical_patient.txt", + "work/upload/data_clinical_sample.txt", + "work/upload/data_cna_gistic.txt", + "work/upload/data_cna_log2.txt", + "work/upload/data_expression.txt", "work/upload/data_mutation_extended.txt", "work/upload/data_segment.txt", - "work/upload/meta_CNA_gistic.txt", - "work/upload/meta_CNA_log2.txt", "work/upload/meta_clinical_patient.txt", "work/upload/meta_clinical_sample.txt", - "work/upload/meta_expression_zscores.txt", + "work/upload/meta_cna_gistic.txt", + "work/upload/meta_cna_log2.txt", + "work/upload/meta_expression.txt", "work/upload/meta_mutation_extended.txt", "work/upload/meta_segment.txt", "work/upload/meta_study.txt", ] actual = list(sorted(cbioportal_export_workflow.get_result_files())) assert actual == expected + + assert cbioportal_export_workflow.check_config() == 0 diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py index 197cb802a..056b56705 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py +++ b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py @@ -701,6 +701,7 @@ def test_ngs_mapping_workflow_steps(ngs_mapping_workflow): "minimap2", "ngs_chew", "star", + "strandedness", "target_coverage_report", ] actual = ngs_mapping_workflow.sub_steps.keys() diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping_processed_fastq.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping_processed_fastq.py index 92ab21943..c62ecebc6 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping_processed_fastq.py +++ b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping_processed_fastq.py @@ -307,8 +307,6 @@ def test_star_step_part_get_output_files(ngs_mapping_workflow): ] = "work/star.{library_name}/out/star.{library_name}.toTranscriptome.bam.md5" expected["output_links"].extend( [ - "output/star.{library_name}/out/star.{library_name}.GeneCounts.tab", - "output/star.{library_name}/out/star.{library_name}.GeneCounts.tab.md5", "output/star.{library_name}/out/star.{library_name}.toTranscriptome.bam", "output/star.{library_name}/out/star.{library_name}.toTranscriptome.bam.md5", ] @@ -344,6 +342,95 @@ def test_star_step_part_get_resource(ngs_mapping_workflow): assert actual == expected, msg_error +# Tests for StrandednessStepPart ------------------------------------------------------------------- + + +def test_strandedness_step_part_infer_get_input_files(ngs_mapping_workflow): + """Tests StrandednessStepPart.get_input_files()""" + # Define expected + expected = { + "bam": "work/{mapper}.{library_name}/out/{mapper}.{library_name}.bam", + } + # Get actual + actual = ngs_mapping_workflow.get_input_files("strandedness", "infer") + assert actual == expected + + +def test_strandedness_step_part_counts_get_input_files(ngs_mapping_workflow): + """Tests StrandednessStepPart.get_input_files()""" + # Define expected + expected = { + "decision": "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.decision.json", + "counts": "work/{mapper}.{library_name}/out/{mapper}.{library_name}.GeneCounts.tab", + } + # Get actual + actual = ngs_mapping_workflow.get_input_files("strandedness", "counts") + assert actual == expected + + +def test_strandedness_step_part_infer_get_output_files(ngs_mapping_workflow): + """Tests StrandednessStepPart.get_output_files()""" + # Define expected + expected = { + "tsv": "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.infer.txt", + "tsv_md5": "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.infer.txt.md5", + "decision": "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.decision.json", + "decision_md5": "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.decision.json.md5", + "output": "output/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.decision.json", + "output_md5": "output/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.decision.json.md5", + "log": "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.log", + "log_md5": "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.log.md5", + "conda_list": "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.conda_list.txt", + "conda_list_md5": "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.conda_list.txt.md5", + "conda_info": "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.conda_info.txt", + "conda_info_md5": "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.conda_info.txt.md5", + } + # Get actual + actual = ngs_mapping_workflow.get_output_files("strandedness", "infer") + assert actual == expected + + +def test_strandedness_step_part_counts_get_output_files(ngs_mapping_workflow): + """Tests StrandednessStepPart.get_output_files()""" + # Define expected + expected = { + "counts": "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.GeneCounts.tab", + "counts_md5": "work/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.GeneCounts.tab.md5", + "output": "output/{mapper}.{library_name}/out/{mapper}.{library_name}.GeneCounts.tab", + "output_md5": "output/{mapper}.{library_name}/out/{mapper}.{library_name}.GeneCounts.tab.md5", + } + # Get actual + actual = ngs_mapping_workflow.get_output_files("strandedness", "counts") + assert actual == expected + + +def test_strandedness_step_part_infer_get_log_file(ngs_mapping_workflow): + """Tests StrandednessStepPart.get_log_file()""" + # Define expected + expected = { + "log": "work/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.log", + "log_md5": "work/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.log.md5", + "conda_info": "work/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.conda_info.txt", + "conda_info_md5": "work/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.conda_info.txt.md5", + "conda_list": "work/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.conda_list.txt", + "conda_list_md5": "work/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.conda_list.txt.md5", + } + # Get actual + actual = ngs_mapping_workflow.get_log_file("strandedness", "infer") + assert actual == expected + + +def test_strandedness_step_part_infer_get_resource(ngs_mapping_workflow): + """Tests StrandednessStepPart.get_resource()""" + # Define expected + expected_dict = {"threads": 1, "time": "01:00:00", "memory": "2G", "partition": "medium"} + # Evaluate + for resource, expected in expected_dict.items(): + msg_error = f"Assertion error for resource '{resource}'." + actual = ngs_mapping_workflow.get_resource("strandedness", "infer", resource) + assert actual == expected, msg_error + + # Tests for Minimap2StepPart ----------------------------------------------------------------------- @@ -567,6 +654,7 @@ def test_ngs_mapping_workflow_steps(ngs_mapping_workflow): "minimap2", "ngs_chew", "star", + "strandedness", "target_coverage_report", ] actual = ngs_mapping_workflow.sub_steps.keys() @@ -703,5 +791,26 @@ def test_ngs_mapping_workflow_files(ngs_mapping_workflow): for ext in ("npz", "npz.md5") for library_name in rna ] + expected += [ + "output/star.{library_name}/strandedness/star.{library_name}.{ext}".format( + library_name=library_name, ext=ext + ) + for ext in ("decision.json", "decision.json.md5") + for library_name in rna + ] + expected += [ + "output/star.{library_name}/log/star.{library_name}.strandedness.{ext}".format( + library_name=library_name, ext=ext + ) + for ext in ( + "log", + "log.md5", + "conda_list.txt", + "conda_list.txt.md5", + "conda_info.txt", + "conda_info.txt.md5", + ) + for library_name in rna + ] assert sorted(ngs_mapping_workflow.get_result_files()) == sorted(expected) diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py index dd66c9deb..fd756d9a4 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py @@ -427,7 +427,9 @@ def test_cnvkit_call_step_part_get_input_files(somatic_targeted_seq_cnv_calling_ def test_cnvkit_call_step_part_get_output_files(somatic_targeted_seq_cnv_calling_workflow): - base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.cns" + base_name_out = ( + "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.call.cns" + ) expected = {"calls": base_name_out, "calls_md5": base_name_out + ".md5"} actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("cnvkit", "call") assert actual == expected @@ -453,13 +455,60 @@ def test_cnvkit_call_step_part_get_resource(somatic_targeted_seq_cnv_calling_wor assert actual == expected, msg_error +# Tests for CnvKitStepPart (postprocess) ---------------------------------------------------------- + + +def test_cnvkit_postprocess_step_part_get_input_files(somatic_targeted_seq_cnv_calling_workflow): + # Define expected + segment_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.segment.cns" + call_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.call.cns" + expected = {"segment": segment_file, "call": call_file} + # Get actual + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) + actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("cnvkit", "postprocess")( + wildcards + ) + assert actual == expected + + +def test_cnvkit_postprocess_step_part_get_output_files(somatic_targeted_seq_cnv_calling_workflow): + base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.cns" + expected = {"final": base_name_out, "final_md5": base_name_out + ".md5"} + actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("cnvkit", "postprocess") + assert actual == expected + + +def test_cnvkit_postprocess_step_part_get_log_file(somatic_targeted_seq_cnv_calling_workflow): + # Define expected + base_name_out = ( + "work/{mapper}.cnvkit.{library_name}/log/{mapper}.cnvkit.postprocess.{library_name}" + ) + expected = get_expected_log_files_dict(base_out=base_name_out) + # Get actual + actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("cnvkit", "postprocess") + assert actual == expected + + +def test_cnvkit_postprocess_step_part_get_resource(somatic_targeted_seq_cnv_calling_workflow): + """Tests CnvKitStepPart.get_resource_usage() - action 'postprocess'""" + # Define expected + expected_dict = {"threads": 1, "time": "03:59:59", "memory": "7680M", "partition": "medium"} + # Evaluate + for resource, expected in expected_dict.items(): + msg_error = f"Assertion error for resource '{resource}'." + actual = somatic_targeted_seq_cnv_calling_workflow.get_resource( + "cnvkit", "postprocess", resource + ) + assert actual == expected, msg_error + + # Tests for CnvKitStepPart (plot) ----------------------------------------------------------------- def test_cnvkit_plot_step_part_get_input_files(somatic_targeted_seq_cnv_calling_workflow): # Define expected cnr_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cnr" - cns_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cns" + cns_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.call.cns" expected = { "cnr": cnr_file, "cns": cns_file, @@ -520,7 +569,9 @@ def test_cnvkit_plot_step_part_get_resource(somatic_targeted_seq_cnv_calling_wor def test_cnvkit_export_step_part_get_input_files(somatic_targeted_seq_cnv_calling_workflow): wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) - expected = {"cns": "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cns"} + expected = { + "cns": "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.call.cns" + } actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("cnvkit", "export")( wildcards ) @@ -567,7 +618,7 @@ def test_cnvkit_export_step_part_get_resource(somatic_targeted_seq_cnv_calling_w def test_cnvkit_report_step_part_get_input_files(somatic_targeted_seq_cnv_calling_workflow): # Define expected cnr_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cnr" - cns_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cns" + cns_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.call.cns" target_file = ( "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.targetcoverage.cnn" ) diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_wgs_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_wgs_cnv_calling.py index 7bec82eaa..35a62fa08 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_wgs_cnv_calling.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_wgs_cnv_calling.py @@ -380,7 +380,9 @@ def test_cnvkit_call_step_part_get_input_files(somatic_wgs_cnv_calling_workflow) def test_cnvkit_call_step_part_get_output_files(somatic_wgs_cnv_calling_workflow): - base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.cns" + base_name_out = ( + "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.call.cns" + ) expected = {"calls": base_name_out, "calls_md5": base_name_out + ".md5"} assert somatic_wgs_cnv_calling_workflow.get_output_files("cnvkit", "call") == expected @@ -405,13 +407,54 @@ def test_cnvkit_call_step_part_get_resource(somatic_wgs_cnv_calling_workflow): assert actual == expected, msg_error +# Tests for CnvKitStepPart (postprocess) ---------------------------------------------------------- + + +def test_cnvkit_postprocess_step_part_get_input_files(somatic_wgs_cnv_calling_workflow): + # Define expected + call_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.call.cns" + expected = {"call": call_file} + # Get actual + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) + actual = somatic_wgs_cnv_calling_workflow.get_input_files("cnvkit", "postprocess")(wildcards) + assert actual == expected + + +def test_cnvkit_postprocess_step_part_get_output_files(somatic_wgs_cnv_calling_workflow): + base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.cns" + expected = {"final": base_name_out, "final_md5": base_name_out + ".md5"} + assert somatic_wgs_cnv_calling_workflow.get_output_files("cnvkit", "postprocess") == expected + + +def test_cnvkit_postprocess_step_part_get_log_file(somatic_wgs_cnv_calling_workflow): + # Define expected + base_name_out = ( + "work/{mapper}.cnvkit.{library_name}/log/{mapper}.cnvkit.postprocess.{library_name}" + ) + expected = get_expected_log_files_dict(base_out=base_name_out) + # Get actual + actual = somatic_wgs_cnv_calling_workflow.get_log_file("cnvkit", "postprocess") + assert actual == expected + + +def test_cnvkit_postprocess_step_part_get_resource(somatic_wgs_cnv_calling_workflow): + """Tests CnvKitStepPart.get_resource_usage() - action 'call'""" + # Define expected + expected_dict = {"threads": 1, "time": "1-00:00:00", "memory": "7680M", "partition": "medium"} + # Evaluate + for resource, expected in expected_dict.items(): + msg_error = f"Assertion error for resource '{resource}'." + actual = somatic_wgs_cnv_calling_workflow.get_resource("cnvkit", "postprocess", resource) + assert actual == expected, msg_error + + # Tests for CnvKitStepPart (plot) ----------------------------------------------------------------- def test_cnvkit_plot_step_part_get_input_files(somatic_wgs_cnv_calling_workflow): # Define expected cnr_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cnr" - cns_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cns" + cns_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.call.cns" expected = { "cnr": cnr_file, "cns": cns_file, @@ -472,7 +515,9 @@ def test_cnvkit_plot_step_part_get_resource(somatic_wgs_cnv_calling_workflow): def test_cnvkit_export_step_part_get_input_files(somatic_wgs_cnv_calling_workflow): wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) - expected = {"cns": "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cns"} + expected = { + "cns": "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.call.cns" + } actual = somatic_wgs_cnv_calling_workflow.get_input_files("cnvkit", "export")(wildcards) assert actual == expected @@ -515,7 +560,7 @@ def test_cnvkit_export_step_part_get_resource(somatic_wgs_cnv_calling_workflow): def test_cnvkit_report_step_part_get_input_files(somatic_wgs_cnv_calling_workflow): # Define expected cnr_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cnr" - cns_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.cns" + cns_file = "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.call.cns" target_file = ( "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.targetcoverage.cnn" ) From 02fa2daa08ee9eaf68d5091765c9fcb03b989820 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 12 Jul 2023 07:28:24 +0200 Subject: [PATCH 02/19] fix: pin dependency joblib of gcnv (#412) --- snappy_wrappers/wrappers/gcnv/environment.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/snappy_wrappers/wrappers/gcnv/environment.yaml b/snappy_wrappers/wrappers/gcnv/environment.yaml index ec3b1f0d7..34c1d5e64 100644 --- a/snappy_wrappers/wrappers/gcnv/environment.yaml +++ b/snappy_wrappers/wrappers/gcnv/environment.yaml @@ -18,6 +18,7 @@ dependencies: - defaults::tensorflow =1.15.0 - conda-forge::scipy =1.0.0 - conda-forge::pymc3 =3.1 + - conda-forge::joblib =1.2.0 - conda-forge::h5py =2.10.0 - conda-forge::keras =2.2.4 - defaults::intel-openmp =2019.4 From 46782861e89b59b471e9bb4d5945af4307f501e9 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 12 Jul 2023 09:01:31 +0200 Subject: [PATCH 03/19] chore: bump mehari to 0.6.1 (#418) --- snappy_wrappers/wrappers/mehari/environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snappy_wrappers/wrappers/mehari/environment.yaml b/snappy_wrappers/wrappers/mehari/environment.yaml index 065eca483..ce59f73a9 100644 --- a/snappy_wrappers/wrappers/mehari/environment.yaml +++ b/snappy_wrappers/wrappers/mehari/environment.yaml @@ -5,7 +5,7 @@ dependencies: - bcftools >=1.9 - htslib >=1.9 - samtools >=1.9 - - mehari ==0.2.1 + - mehari ==0.6.1 - jq - vcfpy - pysam From 6691295e436c30361ca48a26052b8b390464b537 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 17 Jul 2023 09:54:49 +0200 Subject: [PATCH 04/19] chore: bump mehari to 0.6.2 (#419) --- snappy_wrappers/wrappers/mehari/environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snappy_wrappers/wrappers/mehari/environment.yaml b/snappy_wrappers/wrappers/mehari/environment.yaml index ce59f73a9..8461e28b2 100644 --- a/snappy_wrappers/wrappers/mehari/environment.yaml +++ b/snappy_wrappers/wrappers/mehari/environment.yaml @@ -5,7 +5,7 @@ dependencies: - bcftools >=1.9 - htslib >=1.9 - samtools >=1.9 - - mehari ==0.6.1 + - mehari ==0.6.2 - jq - vcfpy - pysam From 04551d5ed26b31e6c822df1a1fe6d83587edec74 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 17 Jul 2023 11:24:45 +0200 Subject: [PATCH 05/19] fix: bump time of ngs_mapping/bam_collect_doc (#394) --- snappy_pipeline/workflows/ngs_mapping/__init__.py | 2 +- tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/snappy_pipeline/workflows/ngs_mapping/__init__.py b/snappy_pipeline/workflows/ngs_mapping/__init__.py index 6e40acacb..0854f0f4b 100644 --- a/snappy_pipeline/workflows/ngs_mapping/__init__.py +++ b/snappy_pipeline/workflows/ngs_mapping/__init__.py @@ -1253,7 +1253,7 @@ def get_resource_usage(self, action): self._check_action(action) return ResourceUsage( threads=1, - time="04:00:00", + time="24:00:00", memory="2G", ) diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py index 056b56705..365b5bce4 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py +++ b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py @@ -679,7 +679,7 @@ def test_generate_doc_files_step_part_run_get_log_file(ngs_mapping_workflow): def test_generate_doc_files_step_part_get_resource(ngs_mapping_workflow): """Tests BamCollectDocStepPart.get_resource()""" - expected_dict = {"threads": 1, "time": "04:00:00", "memory": "2G", "partition": "medium"} + expected_dict = {"threads": 1, "time": "24:00:00", "memory": "2G", "partition": "medium"} for resource, expected in expected_dict.items(): actual = ngs_mapping_workflow.get_resource("bam_collect_doc", "run", resource) assert actual == expected From a40a42da3762f8f06a89d67b46e3f817a2f135bb Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 17 Jul 2023 15:51:28 +0200 Subject: [PATCH 06/19] fix: making compatible with varfish export and mehari (#420) --- .../workflows/varfish_export/__init__.py | 5 ++--- .../mehari/annotate_strucvars/wrapper.py | 20 +++++++++++++++++++ 2 files changed, 22 insertions(+), 3 deletions(-) diff --git a/snappy_pipeline/workflows/varfish_export/__init__.py b/snappy_pipeline/workflows/varfish_export/__init__.py index f4c07d0d5..1211f62dd 100644 --- a/snappy_pipeline/workflows/varfish_export/__init__.py +++ b/snappy_pipeline/workflows/varfish_export/__init__.py @@ -87,9 +87,6 @@ #: Extension of files EXTS = (".tsv.gz", ".tsv.gz.md5") -#: Infixes to use for file name generation -INFIXES = ("gts", "db-infos", "bam-qc") - # TODO: the number of restart times is high because tabix in HTSJDK/Jannovar is flaky... #: Default configuration for the somatic_variant_calling step @@ -391,6 +388,8 @@ def _get_output_files_annotate_strucvars(self): work_paths = { "gts": f"{prefix}.gts.tsv.gz", "gts_md5": f"{prefix}.gts.tsv.gz.md5", + "feature_effects": f"{prefix}.feature-effects.tsv.gz", + "feature_effects_md5": f"{prefix}.feature-effects.tsv.gz.md5", "db_infos": f"{prefix}.db-infos.tsv.gz", "db_infos_md5": f"{prefix}.db-infos.tsv.gz.md5", } diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py index 7ea72deac..55f8d6dbd 100644 --- a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py +++ b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py @@ -92,6 +92,25 @@ tabix -s1 -b2 -e2 -f $TMPDIR/final_for_import.$num.vcf.gz done +cat <<"EOF" > $TMPDIR/feature-effects.tsv +case_id +set_id +sv_uuid +refseq_gene_id +refseq_transcript_id +refseq_transcript_coding +refseq_effect +ensembl_gene_id +ensembl_transcript_id +ensembl_transcript_coding +ensembl_effect +EOF + +cat $TMPDIR/feature-effects.tsv \ +| tr '\n' '\t' \ +| sed -e 's/\t$/\n/g' \ +>{snakemake.output.feature_effects} + # Perform Mehari structural variant annotation. mehari \ annotate \ @@ -113,6 +132,7 @@ # Compute MD5 sums on output files compute-md5 {snakemake.output.db_infos} {snakemake.output.db_infos_md5} compute-md5 {snakemake.output.gts} {snakemake.output.gts_md5} +compute-md5 {snakemake.output.feature_effects} {snakemake.output.feature_effects_md5} # Create output links ----------------------------------------------------------------------------- From 740dda551cf71e49faa31c8fd76ed46aad0dc91c Mon Sep 17 00:00:00 2001 From: ericblanc20 Date: Thu, 27 Jul 2023 07:54:23 +0200 Subject: [PATCH 07/19] fix: fixes multiple issues with the recent cbioportal export changes (#425) Co-authored-by: Manuela Benary --- .../workflows/cbioportal_export/__init__.py | 6 +- .../somatic_variant_calling/__init__.py | 20 +- .../cbioportal/clinical_data/wrapper.py | 8 +- .../cbioportal/generate_cna/environment.yaml | 2 +- .../wrappers/cbioportal/generate_cna/script.R | 2 - .../wrappers/cbioportal/helper_functions.R | 20 +- .../wrappers/cbioportal/merge_tables/script.R | 12 +- .../wrappers/mutect2/filter/wrapper.py | 8 +- .../vcf2maf/vcf_to_table/environment.yaml | 11 +- .../vcf2maf/vcf_to_table/functions.py | 5 +- .../vcf_to_table/hgnc_symbol_to_entrez_id.tsv | 43709 ++++++++++++++++ .../vcf2maf/vcf_to_table/jannovar.yaml | 421 + .../vcf_to_table/protein_mutation_parser.py | 132 +- .../vcf_to_table/variant_classification.py | 78 +- .../vcf_to_table/{config.yaml => vep.yaml} | 2 +- .../wrappers/vcf2maf/vcf_to_table/wrapper.py | 11 +- .../test_workflows_somatic_variant_calling.py | 12 +- 17 files changed, 44343 insertions(+), 116 deletions(-) create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/hgnc_symbol_to_entrez_id.tsv create mode 100644 snappy_wrappers/wrappers/vcf2maf/vcf_to_table/jannovar.yaml rename snappy_wrappers/wrappers/vcf2maf/vcf_to_table/{config.yaml => vep.yaml} (99%) diff --git a/snappy_pipeline/workflows/cbioportal_export/__init__.py b/snappy_pipeline/workflows/cbioportal_export/__init__.py index e42d917a1..a864151fa 100644 --- a/snappy_pipeline/workflows/cbioportal_export/__init__.py +++ b/snappy_pipeline/workflows/cbioportal_export/__init__.py @@ -104,9 +104,9 @@ study_description: REQUIRED # REQUIRED study_name: REQUIRED # REQUIRED study_name_short: REQUIRED # REQUIRED - patient_info: [] # Unimplemented - sample_info: [] # Each entry must have a path & a step associated, see example below - # - step: tumor_mutational_burden + patient_info: {} # Unimplemented + sample_info: {} # Each additional sample column must have a name and a (possibly empty) config attached. + # tumor_mutational_burden: # path: ../tumor_mutational_burden """ diff --git a/snappy_pipeline/workflows/somatic_variant_calling/__init__.py b/snappy_pipeline/workflows/somatic_variant_calling/__init__.py index 92b5bed42..2999aa100 100644 --- a/snappy_pipeline/workflows/somatic_variant_calling/__init__.py +++ b/snappy_pipeline/workflows/somatic_variant_calling/__init__.py @@ -108,8 +108,8 @@ "vcf_md5": ".vcf.gz.md5", "vcf_tbi": ".vcf.gz.tbi", "vcf_tbi_md5": ".vcf.gz.tbi.md5", - "full": ".full.vcf.gz", - "full_md5": ".full.vcf.gz.md5", + "full_vcf": ".full.vcf.gz", + "full_vcf_md5": ".full.vcf.gz.md5", "full_vcf_tbi": ".full.vcf.gz.tbi", "full_vcf_tbi_md5": ".full.vcf.gz.tbi.md5", "txt": ".txt", @@ -122,8 +122,8 @@ "vcf_md5": ".vcf.gz.md5", "vcf_tbi": ".vcf.gz.tbi", "vcf_tbi_md5": ".vcf.gz.tbi.md5", - "full": ".full.vcf.gz", - "full_md5": ".full.vcf.gz.md5", + "full_vcf": ".full.vcf.gz", + "full_vcf_md5": ".full.vcf.gz.md5", "full_vcf_tbi": ".full.vcf.gz.tbi", "full_vcf_tbi_md5": ".full.vcf.gz.tbi.md5", "tar": ".tar.gz", @@ -134,8 +134,8 @@ "vcf_md5": ".vcf.gz.md5", "vcf_tbi": ".vcf.gz.tbi", "vcf_tbi_md5": ".vcf.gz.tbi.md5", - "full": ".full.vcf.gz", - "full_md5": ".full.vcf.gz.md5", + "full_vcf": ".full.vcf.gz", + "full_vcf_md5": ".full.vcf.gz.md5", "full_vcf_tbi": ".full.vcf.gz.tbi", "full_vcf_tbi_md5": ".full.vcf.gz.tbi.md5", }, @@ -675,8 +675,8 @@ def get_output_files(self, action): } if action == "filter": exts = { - "full": ".full.vcf.gz", - "full_md5": ".full.vcf.gz.md5", + "full_vcf": ".full.vcf.gz", + "full_vcf_md5": ".full.vcf.gz.md5", "full_vcf_tbi": ".full.vcf.gz.tbi", "full_vcf_tbi_md5": ".full.vcf.gz.tbi.md5", "vcf": ".vcf.gz", @@ -818,8 +818,8 @@ class Strelka2StepPart(SomaticVariantCallingStepPart): "vcf_md5": ".vcf.gz.md5", "vcf_tbi": ".vcf.gz.tbi", "vcf_tbi_md5": ".vcf.gz.tbi.md5", - "full": ".full.vcf.gz", - "full_md5": ".full.vcf.gz.md5", + "full_vcf": ".full.vcf.gz", + "full_vcf_md5": ".full.vcf.gz.md5", "full_vcf_tbi": ".full.vcf.gz.tbi", "full_vcf_tbi_md5": ".full.vcf.gz.tbi.md5", "stats": ".tsv", diff --git a/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py b/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py index 65aae5b9a..38788eacf 100644 --- a/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py +++ b/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py @@ -80,15 +80,13 @@ def write_clinical_samples_tsv(donors): """ sample_info_getters = [] - for extra_info in snakemake.config["step_config"]["cbioportal_export"]["sample_info"]: - step = extra_info["step"] + config = snakemake.config["step_config"]["cbioportal_export"] + for step, extra_info in config["sample_info"].items(): if step == "tumor_mutational_burden": sample_info_getters.append( SampleInfoTMB( extra_info, - somatic_variant_tool=snakemake.config["step_config"]["cbioportal_export"][ - "somatic_variant_calling_tool" - ], + somatic_variant_tool=config["somatic_variant_calling_tool"], ) ) else: diff --git a/snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml b/snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml index 1f257fe3a..869a5e0d8 100644 --- a/snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml +++ b/snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml @@ -1,4 +1,4 @@ -name: merge_tables +name: generate_cna channels: - conda-forge diff --git a/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R b/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R index 6438e6b83..87fe716ae 100644 --- a/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R +++ b/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R @@ -1,5 +1,3 @@ -require(magrittr) - #' Compute discrete copy number & log2 on genes #' #' @param fn names of the cns file diff --git a/snappy_wrappers/wrappers/cbioportal/helper_functions.R b/snappy_wrappers/wrappers/cbioportal/helper_functions.R index 2858fdfb9..4162dcfb8 100644 --- a/snappy_wrappers/wrappers/cbioportal/helper_functions.R +++ b/snappy_wrappers/wrappers/cbioportal/helper_functions.R @@ -1,5 +1,3 @@ -require(magrittr) - #' Extracts the feature names & one column of values from tab-delimited sample files #' and return a data.frame with the values for each sample in the columns, and #' the feature names as row name. @@ -34,7 +32,7 @@ read_sample_files <- function(fns, featureCol, valueCol, header=TRUE) { if (is.null(tbl)) { tbl <- tmp } else { - tbl <- tbl %>% dplyr::full_join(tmp, by=featureCol) + tbl <- tbl |> dplyr::full_join(tmp, by=featureCol) } } tbl <- tbl[!grepl("_PAR_Y$", tbl[[featureCol]]),,drop=FALSE] @@ -75,7 +73,7 @@ map_feature_id <- function(mat, mappings, from, to, method=c("sum", "max", "maxa if (!all(c(from, to) %in% colnames(mappings))) stop("Feature id type ", from, " or ", to, " not in mappings table") - mappings <- mappings[,c(from, to)] %>% dplyr::distinct() + mappings <- mappings[,c(from, to)] |> dplyr::distinct() mappings <- mappings[mappings[[from]] %in% rownames(mat),,drop=FALSE] n <- sum(rownames(mat) %in% mappings[[from]]) @@ -189,7 +187,7 @@ get_id_mappings <- function(org_obj, verbose=FALSE) { if (verbose) cat("Gene id mappings taken from file ", org_obj) id_mappings <- read.table(org_obj, sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE, quote="", comment="") if (all(c("hgnc_symbol", "ensembl_canonical_gene", "entrez_gene_id") %in% colnames(id_mappings))) - id_mappings <- id_mappings %>% + id_mappings <- id_mappings |> dplyr::select(ENSEMBL=ensembl_canonical_gene, SYMBOL=hgnc_symbol, ENTREZ_ID=entrez_gene_id) stopifnot(all(c("ENSEMBL", "SYMBOL", "ENTREZ_ID") %in% colnames(id_mappings))) id_mappings <- id_mappings[,c("ENSEMBL", "SYMBOL", "ENTREZ_ID")] @@ -205,12 +203,12 @@ get_id_mappings <- function(org_obj, verbose=FALSE) { ) } } - id_mappings <- id_mappings %>% - dplyr::select(ENSEMBL, SYMBOL, ENTREZ_ID) %>% - dplyr::mutate(ENTREZ_ID=as.character(ENTREZ_ID)) %>% - dplyr::filter(!is.na(ENSEMBL) & ENSEMBL!="") %>% - dplyr::filter(!is.na(SYMBOL) & SYMBOL!="") %>% - dplyr::filter(!is.na(ENTREZ_ID) & ENTREZ_ID!="" & grepl("^[0-9]+$", ENTREZ_ID)) %>% + id_mappings <- id_mappings |> + dplyr::select(ENSEMBL, SYMBOL, ENTREZ_ID) |> + dplyr::mutate(ENTREZ_ID=as.character(ENTREZ_ID)) |> + dplyr::filter(!is.na(ENSEMBL) & ENSEMBL!="") |> + dplyr::filter(!is.na(SYMBOL) & SYMBOL!="") |> + dplyr::filter(!is.na(ENTREZ_ID) & ENTREZ_ID!="" & grepl("^[0-9]+$", ENTREZ_ID)) |> dplyr::distinct() id_mappings diff --git a/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R b/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R index 8d1a26ddf..0b0aada8a 100644 --- a/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R +++ b/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R @@ -1,5 +1,3 @@ -require(magrittr) - #' Read & merge sample files into cBioPortal gene-based data table. #' #' Used for expression tables, log2 CNA, pseudo-Gistic table. @@ -39,7 +37,7 @@ merge_tables <- function(fns, mappings, type=c("log2", "gistic", "segment", "exp } if (type == "gistic") { - stopifnot(all(c("pipeline_id", "amplification") %in% names(args))) + stopifnot(all(c("pipeline_id") %in% names(args))) # Copy numbers (in "cn" column) are transformed into (pseudo-) gistic codes: # 0: Deep deletion, 1: heterozygous deletion, 2: copy number neutral, 3: gain, 4: amplification # In https://doi.org/10.1038/s41586-022-04738-6, the amplification is defined as @@ -59,7 +57,7 @@ merge_tables <- function(fns, mappings, type=c("log2", "gistic", "segment", "exp } if (type == "log2") { - stopifnot(all(c("pipeline_id") %in% names(args))) + stopifnot(all(c("pipeline_id", "amplification") %in% names(args))) tmp <- read_sample_files(fns, args$pipeline_id, "log2") method <- "max" } @@ -107,6 +105,10 @@ merge_segments <- function(fns) { for (sample_id in names(fns)) { cat("Loading", fns[sample_id], "for sample", sample_id, "\n") tmp <- read.table(fns[sample_id], sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE) + if (!all(col_names %in% colnames(tmp))) { + i <- match(names(col_names), colnames(tmp)) + if (any(!is.na(i))) colnames(tmp)[i[!is.na(i)]] <- col_names[!is.na(i)] + } stopifnot(all(names(col_names) %in% colnames(tmp))) tmp <- tmp[,names(col_names)] colnames(tmp) <- col_names @@ -147,7 +149,7 @@ compute_rpkm <- function(counts, tx_obj=TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb. if (verbose) cat("Create DESeq2 object ... ") genes <- GenomicFeatures::exonsBy(tx_obj, "gene") genes <- genes[names(genes) %in% rownames(counts)] - counts <- counts[names(genes),] + counts <- counts[names(genes),,drop=FALSE] donors <- data.frame(Donor=colnames(counts), stringsAsFactors=FALSE) dds <- DESeq2::DESeqDataSetFromMatrix(counts, colData=donors, design=as.formula("~ 1"), rowRanges=genes) if (verbose) cat("Done\n") diff --git a/snappy_wrappers/wrappers/mutect2/filter/wrapper.py b/snappy_wrappers/wrappers/mutect2/filter/wrapper.py index 2b7b8e186..cd1beb527 100644 --- a/snappy_wrappers/wrappers/mutect2/filter/wrapper.py +++ b/snappy_wrappers/wrappers/mutect2/filter/wrapper.py @@ -84,13 +84,13 @@ --ob-priors $tmpdir/read-orientation-model.tar.gz \ --stats {snakemake.input.stats} \ --variant $tmpdir/in.vcf \ - --output {snakemake.output.full} + --output {snakemake.output.full_vcf} # Index & move to final dest -tabix -f {snakemake.output.full} +tabix -f {snakemake.output.full_vcf} # Keep only PASS variants in main output -bcftools view -i 'FILTER="PASS"' -O z -o {snakemake.output.vcf} {snakemake.output.full} +bcftools view -i 'FILTER="PASS"' -O z -o {snakemake.output.vcf} {snakemake.output.full_vcf} tabix -f {snakemake.output.vcf} pushd $(dirname {snakemake.output.vcf}) @@ -98,7 +98,7 @@ md5sum $fn > $fn.md5 fn=$(basename {snakemake.output.vcf_tbi}) md5sum $fn > $fn.md5 -fn=$(basename {snakemake.output.full}) +fn=$(basename {snakemake.output.full_vcf}) md5sum $fn > $fn.md5 fn=$(basename {snakemake.output.full_vcf_tbi}) md5sum $fn > $fn.md5 diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml index 8a155a981..794d134f1 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml @@ -1,7 +1,8 @@ channels: -- bioconda -- conda-forge + - conda-forge + - bioconda + dependencies: -- python >=3.8 -- vcfpy -- ruamel.yaml + - python >=3.8 + - vcfpy + - ruamel.yaml diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/functions.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/functions.py index 216e27cfb..c3e17567a 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/functions.py +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/functions.py @@ -8,7 +8,7 @@ from common_functions import calc_end_pos, minimize_mutation, strip_sequence_version, variant_type import exceptions from protein_mutation_parser import parse_protein_mutation -from variant_classification import variant_classification +from variant_classification import variant_classification_jannovar, variant_classification_vep # from action import Action @@ -27,7 +27,8 @@ def __init__(self, config: typing.Dict[str, typing.Any]): self.compiled["strip_sequence_version"] = strip_sequence_version self.compiled["variant_type"] = variant_type self.compiled["parse_protein_mutation"] = parse_protein_mutation - self.compiled["variant_classification"] = variant_classification + self.compiled["variant_classification_vep"] = variant_classification_vep + self.compiled["variant_classification_jannovar"] = variant_classification_jannovar for col_name, col_def in config["output"].items(): if "function" in col_def and not col_def["function"] in self.compiled: diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/hgnc_symbol_to_entrez_id.tsv b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/hgnc_symbol_to_entrez_id.tsv new file mode 100644 index 000000000..d49e7b460 --- /dev/null +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/hgnc_symbol_to_entrez_id.tsv @@ -0,0 +1,43709 @@ +A1BG 1 +A1BG-AS1 503538 +A1CF 29974 +A2M 2 +A2M-AS1 144571 +A2ML1 144568 +A2ML1-AS1 100874108 +A2ML1-AS2 106478979 +A2MP1 3 +A3GALT2 127550 +A4GALT 53947 +A4GNT 51146 +AAAS 8086 +AACS 65985 +AACSP1 729522 +AADAC 13 +AADACL2 344752 +AADACL2-AS1 101928142 +AADACL3 126767 +AADACL4 343066 +AADACP1 201651 +AADAT 51166 +AAGAB 79719 +AAK1 22848 +AAMDC 28971 +AAMP 14 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b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/jannovar.yaml @@ -0,0 +1,421 @@ +annotation: # Definition of annotations from jannovar + id: "ANN" # INFO field ID (unless change with --vcf_info_field option) + allele: "Allele" # Variant used to calculate consequence (https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#defaultout) + extract: "^Functional annotations:'(.+)'$" # Regular expression to extract annotation names from the description of INFO field. The annotation names are in group 1 + split: "\\|" # Regular expression to split annotations (& annotation names) from the INFO field + minimize: True # Variant minimization applied by VEP (see https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#colocated) + + +output: # Output columns definition + + Hugo_Symbol: # Column name to output HGNC Symbol + input: # Required input + - set: "annotation" # The "SYMBOL" annotation column contains the requested information + column: "Gene_Name" + on_missing: skip # Genomic regions variants are not attached to genes, skip them on output + + Entrez_Gene_Id: # Column name to output NCBI ID + input: + - set: "annotation" # VEP doesn't provide NCBI gene ids (formerly ENTREZ gene ids) + column: "Gene_Name" # The column value is obtained by mapping the HGNC symbol + function: "map" # The "map" function is invoked with one input (the annotation SYMBOL), + args: # and one named argument, the mapping file (fixed for all variants) + filename: "hgnc_symbol_to_entrez_id.tsv" + on_missing: default # When no Entrez id is not for a symbol, the value is set to 0 + default: 0 + + Center: # Sequencing or processing center name + input: + - set: "constant" # The value is defined on the (optional) command-line arguments + column: "Center" # The argument is --Center + on_missing: default + default: "BIH" # When missing, the value "BIH" is used. + + NCBI_Build: + input: + - set: "constant" + column: "NCBI_Build" + on_missing: default + default: "GRCh37" + + Chromosome: # Sequence name + input: + - set: "fixed" # The input is taken from the vcf fixed field "CHROM" + column: "CHROM" + on_missing: stop # This field must be present. When absent, the program stops with an error + + Start_Position: # Position of the start of the variant. + input: # Note that vcf2maf.pl transforms the variant (position & allele sequences) + - set: "fixed" # to minimize them (see https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html). + column: "POS" # This is *NOT* compatible with variant normalization as defined in + on_missing: stop # https://genome.sph.umich.edu/wiki/Variant_Normalization + - set: "variant" # The function "minimize_mutation" performs variant minimization, + column: "REF" # so the output is (should be) identical to anything produced by vcf2maf.pl + on_missing: stop # If the user wants to keep the variant definition as in the vcf file, + - set: "variant" # the configuration should be updated, and the "Start_Position" column should be + column: "ALT" # defined similarly to the "Chromosome" column, simply copying the contents of + on_missing: stop # the vcf's "POS" column. + function: "minimize_mutation" # The same applies to the columns describing the reference & alternate allele sequences, + args: # "Reference_Allele", "Tumor_Seq_Allele1" & "Tumor_Seq_Allele2", which should be + return_value: "pos" # copied from vcf columns "REF", "REF" & "ALT" respectively. + on_missing: stop + + End_Position: # Position of the end of the variant + input: # This information is missing from the vcf + - set: "fixed" # It is reconstituted from the start position, and the lengths of the reference & alternative alleles + column: "POS" # The program stop if either values are missing. + on_missing: stop + - set: "variant" # If the user want to keep the variant definition as in the vcf file, + column: "REF" # another function is provided, which doesn't alter the variant's starting position, + on_missing: stop # and simply computes the end of the variant locus as: + - set: "variant" # POS + length(reference allele sequence) - 1 for substitutions & deletions, and + column: "ALT" # POS + 1 for insertions + on_missing: stop + function: "minimize_mutation" # This alternative function is "calc_end_pos". + args: # It takes the same input as "minimize_mutation", but with additional arguments. + return_value: "end" # "calc_end_pos" assumes that the variant is normalized. + on_missing: stop + + Strand: + input: + - set: "constant" + column: "Strand" + on_missing: default + default: "+" + + Variant_Classification: # Variant classification + input: # Maps the jannovar variant classification + - set: "annotation" + column: "Annotation" + - set: "variant" + column: "REF" + - set: "variant" + column: "ALT" + function: "variant_classification_jannovar" + on_missing: default + default: "" + + Variant_Type: # Variant type (SNP/DNP/TNP/ONP/INS/DEL). + input: # The type "Consolidated" is not implemented. + - set: "variant" + column: "REF" # The function "variant_type" outputs the type based only on the length of + - set: "variant" # reference & alternative allele sequences. + column: "ALT" + function: "variant_type" + on_missing: default + default: "" + + Reference_Allele: # Reference allele (should be identical to the reference genome at the locus) + input: # Rather, it is taken from the normal homozygous allele. + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "REF" column is simply copied + column: "REF" # to the output column ("Reference_Allele"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "ref" + on_missing: stop + + Tumor_Seq_Allele1: # Unmutated allele in the tumor sample + input: + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "REF" column is simply copied + column: "REF" # to the output column ("Tumor_Seq_Allele1"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "ref" + on_missing: stop + + Tumor_Seq_Allele2: # Mutated allele in the tumor sample + input: + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "ALT" column is simply copied + column: "REF" # to the output column ("Tumor_Seq_Allele2"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "alt" + on_missing: stop + + dbSNP_RS: # dbSNP references + input: # Note that VEP also includes COSMIC references in that field. + - set: "constant" # TODO: create a function that parses the vcf field, extracts only the dbSNP + column: "Existing_variation" # ids and collapses them into a single strings separated by semicolumns. + on_missing: default + default: "" + + dbSNP_Val_Status: + input: + - set: "constant" + column: "dbSNP_Val_Status" + on_missing: default + default: "" + + Tumor_Sample_Barcode: + input: + - set: "constant" + column: "tumor_id" + on_missing: default + default: "tumor" + + Matched_Normal_Sample_Barcode: + input: + - set: "constant" + column: "normal_id" + on_missing: default + default: "normal" + + Match_Norm_Seq_Allele1: # Match normal allele1. + input: # Should be identical to "Tumor_Allele1", but instead is set to the reference genome sequence + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "REF" column is simply copied + column: "REF" # to the output column ("Tumor_Seq_Allele1"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "ref" + on_missing: stop + + Match_Norm_Seq_Allele2: # Match normal allele2 (the allele mutated in the tumor) + input: + - set: "fixed" + column: "POS" # The configuration is set so that the vcf2maf.pl behaviour is reproduced. + on_missing: stop # If the user want to keep the variant definition as in the vcf file instead, + - set: "variant" # the configuration should be set so that the vcf "REF" column is simply copied + column: "REF" # to the output column ("Tumor_Seq_Allele1"). + on_missing: stop + - set: "variant" + column: "ALT" + on_missing: stop + function: "minimize_mutation" + args: + return_value: "ref" + on_missing: stop + + Tumor_Validation_Allele1: # Validation not implemented. All fields are empty + input: + - set: "constant" + column: "Tumor_Validation_Allele1" + on_missing: default + default: "" + + Tumor_Validation_Allele2: # Validation not implemented. All fields are empty + input: + - set: "constant" + column: "Tumor_Validation_Allele2" + on_missing: default + default: "" + + Match_Norm_Validation_Allele1: # Validation not implemented. All fields are empty + input: + - set: "constant" + column: "Match_Norm_Validation_Allele1" + on_missing: default + default: "" + + Match_Norm_Validation_Allele2: # Validation not implemented. All fields are empty + input: + - set: "constant" + column: "Match_Norm_Validation_Allele1" + on_missing: default + default: "" + + Verification_Status: + input: + - set: "constant" + column: "Verification_Status" + on_missing: default + default: "Unknown" + + Validation_Status: + input: + - set: "constant" + column: "Validation_Status" + on_missing: default + default: "Unknown" + + Mutation_Status: + input: + - set: "constant" + column: "Mutation_Status" + on_missing: default + default: "Somatic" + + Sequencing_Phase: + input: + - set: "constant" + column: "Sequencing_Phase" + on_missing: default + default: "Unknown" + + Sequence_Source: + input: + - set: "constant" + column: "Sequence_Source" + on_missing: default + default: "Unknown" + + Validation_Method: + input: + - set: "constant" + column: "Validation_Method" + on_missing: default + default: "Unknown" + + Score: + input: + - set: "constant" + column: "Score" + on_missing: default + default: "" + + BAM_File: + input: + - set: "constant" + column: "BAM_File" + on_missing: default + default: "" + + Sequencer: + input: + - set: "constant" + column: "Sequencer" + on_missing: default + default: "" + + Tumor_Sample_UUID: + input: + - set: "constant" + column: "Tumor_Sample_UUID" + on_missing: default + default: "" + + Matched_Norm_Sample_UUID: + input: + - set: "constant" + column: "Matched_Norm_Sample_UUID" + on_missing: default + default: "" + + # Start of supplementary columns not defined in ----------------------------------------------- + # https://docs.gdc.cancer.gov/Encyclopedia/pages/Mutation_Annotation_Format_TCGAv2/ ----------- + + # The columns belows are all defined in ------------------------------------------------------- + # https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/#notes-about-gdc-maf-implementation + # Note that some columns are commented out, and will not be part of the output. --------------- + + HGVSc: + input: + - set: "annotation" + column: "HGVS.c" + on_missing: default + default: "" + + HGVSp: + input: + - set: "annotation" + column: "HGVS.p" + on_missing: default + default: "" + + HGVSp_Short: # Short version of the protein mutation defined in + input: # VEP annotation column "HGVSp" + - set: "annotation" + column: "HGVS.p" # The function "parse_protein_mutation" removed the + function: "parse_protein_mutation" # sequence identifier, and replaces 3-letter amino-acid codes + args: # with single letter amino-acid codes. + add_sequence: False # The arguments "add_sequence", "want_short" & "want_long" + want_short: True # allow the user to change this behaviour. + want_long: False + on_missing: skip + # default: "" + + Transcript_ID: + input: + - set: "annotation" + column: "Feature_ID" + on_missing: default + default: "" + + Exon_Number: # VEP annotates the exon number & the total number of exons in the transcript. + input: # It is unclear what the MAF documentation requires. + - set: "annotation" + column: "EXON" + on_missing: default + default: "" + + t_depth: # Read depth in the tumor sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "tumor" + column: "DP" + on_missing: default + default: "" + + t_ref_count: # Reference allele read counts in the tumor sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "tumor" + column: "AD[REF]" + on_missing: default + default: "" + + t_alt_count: # Alternative allele read counts in the tumor sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "tumor" + column: "AD[0]" + on_missing: default + default: "" + + n_depth: # Read depth in the normal sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "normal" + column: "DP" + on_missing: default + default: "" + + n_ref_count: # Reference allele read counts in the normal sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "normal" + column: "AD[REF]" + on_missing: default + default: "" + + n_alt_count: # Alternative allele read counts in the normal sample. + input: # The VCF "FORMAT" fields are those used by "Mutect2" + - set: "format" + sample: "normal" + column: "AD[0]" + on_missing: default + default: "" + + Protein_Position: + input: + - set: "annotation" + column: "Protein_position" + on_missing: default + default: "" diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py index 9b60c721e..2d0baaa31 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py @@ -212,15 +212,15 @@ def _build_protein_pattern(): + "(" + "|".join( [ - "0", # No group, but seq in 2 - substitution, # 3: ref, 4: position, 5: alt - duplication, # 6: start, 7: start pos, 9: end, 10: end pos - deletion, # 11: start, 12: start pos, 14: end, 15: end pos - insertion, # 16: start, 17: start pos, 18: end, 19: end pos (=start pos + 1), 20+22: insertion - delins, # 23: start, 24: start pos, 26: end, 27: end pos, 28+30: insertion - frameshift, # 31: start, 33: start pos, 33: end, 35: ter pos - extensionN, # 37: pos (negative number) - extensionC, # 39: pos, 40: alt, 42: ter pos + "(0|=|\?)", # noqa: W605 + substitution, # 4: ref, 5: position, 6: alt + duplication, # 7: start, 8: start pos, 10: end, 11: end pos + deletion, # 12: start, 13: start pos, 15: end, 16: end pos + insertion, # 17: start, 18: start pos, 19: end, 20: end pos (=start pos + 1), 21+23: insertion + delins, # 24: start, 25: start pos, 27: end, 28: end pos, 29+31: insertion + frameshift, # 32: start, 34: start pos, 34: end, 36: ter pos + extensionN, # 38: pos (negative number) + extensionC, # 40: pos, 41: alt, 43: ter pos ] ) + ")" @@ -285,80 +285,98 @@ def _one_or_interval(groups, i0, want_short=True, want_long=False): def _parse_mutation_groups(groups, want_short=True, want_long=False): - if groups[2] == "0": - rslt = "0" + iGroup = 3 + if groups[iGroup] and groups[iGroup] in ("0", "=", "?"): + return groups[iGroup] + iGroup += 1 - elif groups[3] is not None: + if groups[iGroup] is not None: # Substitutions - rslt = ( - _aa(groups[3], want_short=want_short, want_long=want_long) - + groups[4] - + _aa(groups[5], want_short=want_short, want_long=want_long) + # print("DEBUG- substitution: groups = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(4, 7)]))) + return ( + _aa(groups[iGroup], want_short=want_short, want_long=want_long) + + groups[iGroup + 1] + + _aa(groups[iGroup + 2], want_short=want_short, want_long=want_long) ) - # print("DEBUG- substitution: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(3, 6)]), rslt)) + iGroup += 3 - elif groups[6] is not None: + if groups[iGroup] is not None: # Duplications - rslt = _one_or_interval(groups, 6, want_short=want_short, want_long=want_long) + "dup" - # print("DEBUG- duplication: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(6, 11)]), rslt)) + # print("DEBUG- duplication: groups = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(8, 12)]))) + return _one_or_interval(groups, iGroup, want_short=want_short, want_long=want_long) + "dup" + iGroup += 5 - elif groups[11] is not None: + if groups[iGroup] is not None: # Deletions - rslt = _one_or_interval(groups, 11, want_short=want_short, want_long=want_long) + "del" - # print("DEBUG- deletion: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(11, 16)]), rslt)) + # print("DEBUG- deletion: groups = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(12, 17)]))) + return _one_or_interval(groups, iGroup, want_short=want_short, want_long=want_long) + "del" + iGroup += 5 - elif groups[16] is not None: + if groups[iGroup] is not None: # Insertions - is_long = _is_long(groups[16]) - rslt = ( - _interval(groups, 16, want_short=want_short, want_long=want_long) + # print("DEBUG- insertion: groups = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(17, 24)]))) + is_long = _is_long(groups[iGroup]) + return ( + _interval(groups, iGroup, want_short=want_short, want_long=want_long) + "ins" - + _many_aas(groups[20], want_short=want_short, want_long=want_long, is_long=is_long) - + _aa(groups[22], want_short=want_short, want_long=want_long) + + _many_aas( + groups[iGroup + 4], want_short=want_short, want_long=want_long, is_long=is_long + ) + + _aa(groups[iGroup + 6], want_short=want_short, want_long=want_long) ) - # print("DEBUG- insertion: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(16, 23)]), rslt)) + iGroup += 7 - elif groups[23] is not None: + if groups[iGroup] is not None: # Deletion-insertions - is_long = _is_long(groups[23]) - rslt = ( - _one_or_interval(groups, 23, want_short=want_short, want_long=want_long) + # print("DEBUG- delins: groups = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(24, 32)]))) + is_long = _is_long(groups[iGroup]) + return ( + _one_or_interval(groups, iGroup, want_short=want_short, want_long=want_long) + "delins" - + _many_aas(groups[28], want_short=want_short, want_long=want_long, is_long=is_long) - + _aa(groups[30], want_short=want_short, want_long=want_long) + + _many_aas( + groups[iGroup + 5], want_short=want_short, want_long=want_long, is_long=is_long + ) + + _aa(groups[iGroup + 7], want_short=want_short, want_long=want_long) ) - # print("DEBUG- delins: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(23, 31)]), rslt)) + iGroup += 8 - elif groups[31] is not None: + if groups[iGroup] is not None: # Frameshift - rslt = ( - _aa(groups[31], want_short=want_short, want_long=want_long) - + groups[32] - + _aa(groups[33], want_short=want_short, want_long=want_long) + # print("DEBUG- frameshift: groups = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(32, 37)]))) + return ( + _aa(groups[iGroup], want_short=want_short, want_long=want_long) + + groups[iGroup + 1] + + _aa(groups[iGroup + 2], want_short=want_short, want_long=want_long) + "fs" - + _aa(groups[34], want_short=want_short, want_long=want_long) - + groups[35] + + _aa(groups[iGroup + 3], want_short=want_short, want_long=want_long) + + groups[iGroup + 4] ) - # print("DEBUG- frameshift: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(31, 36)]), rslt)) + iGroup += 5 - elif groups[36] is not None: + if groups[iGroup] is not None: # Extension N terminus - rslt = _aa(groups[36], want_short=want_short, want_long=want_long) + "1ext" + groups[37] - # print("DEBUG- extension N: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(36, 38)]), rslt)) + # print("DEBUG- extension N: groups = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(37, 39)]))) + return ( + _aa(groups[iGroup], want_short=want_short, want_long=want_long) + + "1ext" + + groups[iGroup + 1] + ) + iGroup += 3 - elif groups[38] is not None: + if groups[iGroup] is not None: # Extension C terminus - rslt = ( - _aa(groups[38], want_short=want_short, want_long=want_long) - + groups[39] - + _aa(groups[40], want_short=want_short, want_long=want_long) + # print("DEBUG- extension C: groups = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(39, 44)]))) + return ( + _aa(groups[iGroup], want_short=want_short, want_long=want_long) + + groups[iGroup + 1] + + _aa(groups[iGroup + 2], want_short=want_short, want_long=want_long) + "ext" - + _aa(groups[41], want_short=want_short, want_long=want_long) - + groups[42] + + _aa(groups[iGroup + 3], want_short=want_short, want_long=want_long) + + groups[iGroup + 4] ) - # print("DEBUG- extension C: groups = {}, rslt = {}".format(", ".join(["{}={}".format(i, groups[i]) for i in range(38, 43)]), rslt)) + iGroup += 5 - return rslt + return "" def _parse_one_mutation(mut, want_short=True, want_long=False, add_sequence=False): diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/variant_classification.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/variant_classification.py index 7d279c98e..62bf85891 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/variant_classification.py +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/variant_classification.py @@ -60,10 +60,42 @@ ("feature_elongation", "Targeted_Region"), ("feature_truncation", "Targeted_Region"), ) -variant_classes_all = variant_classes_vcftomaf + variant_classes_vep109 +variant_classes_vep = variant_classes_vcftomaf + variant_classes_vep109 + +variant_classes_jannovar = ( + ("3_prime_UTR_exon_variant", "3'UTR"), + ("3_prime_UTR_intron_variant", "3'UTR"), + ("5_prime_UTR_exon_variant", "5'UTR"), + ("5_prime_UTR_intron_variant", "5'UTR"), + ("coding_transcript_intron_variant", "Intron"), + ("complex_substitution", "Targeted_Region"), + ("direct_tandem_duplication", "In_Frame_Ins"), + ("disruptive_inframe_deletion", "Frame_Shift_Del"), + ("disruptive_inframe_insertion", "Frame_Shift_Ins"), + ("downstream_gene_variant", "3'Flank"), + ("frameshift_elongation", "Frame_Shift_Ins"), + ("frameshift_truncation", "Frame_Shift_Del"), + # + ("inframe_deletion", "In_Frame_Del"), + ("inframe_insertion", "In_Frame_Ins"), + ("intergenic_variant", "IGR"), + ("missense_variant", "Missense_Mutation"), + ("mnv", "Missense_Mutation"), + ("non_coding_transcript_exon_variant", "RNA"), + ("non_coding_transcript_intron_variant", "RNA"), + ("splice_acceptor_variant", "Splice_Region"), + ("splice_donor_variant", "Splice_Region"), + ("splice_region_variant", "Splice_Region"), + ("start_lost", "Translation_Start_Site"), + ("stop_gained", "Nonsense_Mutation"), + ("stop_lost", "Nonstop_Mutation"), + ("stop_retained_variant", "Silent"), + ("synonymous_variant", "Silent"), + ("upstream_gene_variant", "5'Flank"), +) -def variant_classification(x, args=None): +def variant_classification_vep(x, args=None): if x is None: return None assert isinstance(x, list) and len(x) == 4 @@ -93,7 +125,7 @@ def variant_classification(x, args=None): inFrame = (abs(len(ref) - len(alt)) % 3) == 0 found = False - for (k, v) in variant_classes_all: + for (k, v) in variant_classes_vep: if ensembl == k: tcga.append(v) found = True @@ -123,3 +155,43 @@ def variant_classification(x, args=None): tcga.append("Targeted_Region") return tcga + + +def variant_classification_jannovar(x, args=None): + if x is None: + return None + assert isinstance(x, list) and len(x) == 3 + if x[0] is None: + return None + assert isinstance(x[0], list) and len(x[0]) > 0 + assert isinstance(x[1], list) and len(x[1]) == len(x[0]) + assert isinstance(x[2], list) and len(x[2]) == len(x[0]) + tcga = list() + for i in range(len(x[0])): + jannovar = x[0][i] + if jannovar is None: + tcga.append(None) + continue + jannovar = jannovar.split("&")[0] + ref = x[1][i].replace("-", "") + alt = x[2][i].replace("-", "") + indel = "insertion" if len(ref) < len(alt) else "deletion" + # inFrame = (abs(len(ref) - len(alt)) % 3) == 0 + + found = False + for (k, v) in variant_classes_jannovar: + if jannovar == k: + tcga.append(v) + found = True + break + if found: + continue + + if indel == "deletion" and jannovar == "frameshift_variant": + tcga.append("Frame_Shift_Del") + elif indel == "insertion" and jannovar == "frameshift_variant": + tcga.append("Frame_Shift_Ins") + else: + tcga.append("Targeted_Region") + + return tcga diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/config.yaml b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/vep.yaml similarity index 99% rename from snappy_wrappers/wrappers/vcf2maf/vcf_to_table/config.yaml rename to snappy_wrappers/wrappers/vcf2maf/vcf_to_table/vep.yaml index f442a1e04..d22820b89 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/config.yaml +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/vep.yaml @@ -93,7 +93,7 @@ output: # Output columns definitio column: "REF" - set: "variant" # Note that a simple mapping was not possible, because the algorithm requires column: "ALT" # the knowledge of substitution, insertion or deletion to assign some values. - function: "variant_classification" + function: "variant_classification_vep" on_missing: default default: "" diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py index d48c77bae..620514f32 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py @@ -10,7 +10,16 @@ config = snakemake.config["step_config"][step] vcf_to_table = os.path.join(os.path.dirname(os.path.realpath(__file__)), "vcf_to_table.py") -vcf_to_table_config = os.path.join(os.path.dirname(os.path.realpath(__file__)), "config.yaml") +if config["somatic_variant_annotation_tool"] == "vep": + vcf_to_table_config = os.path.join(os.path.dirname(os.path.realpath(__file__)), "vep.yaml") +elif config["somatic_variant_annotation_tool"] == "jannovar_annotate_somatic_vcf": + vcf_to_table_config = os.path.join(os.path.dirname(os.path.realpath(__file__)), "jannovar.yaml") +else: + raise Exception( + "vcf to maf conversion error: unimplemented conversion from annotation tool {}".format( + config["somatic_variant_annotation_tool"] + ) + ) params = snakemake.params.args diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_calling.py index 6795e9e7b..d13bd9284 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_calling.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_calling.py @@ -139,8 +139,8 @@ def test_mutect_step_part_get_output_files(somatic_variant_calling_workflow): "vcf_md5": base_name_out + ".vcf.gz.md5", "full_vcf_tbi": base_name_out + ".full.vcf.gz.tbi", "full_vcf_tbi_md5": base_name_out + ".full.vcf.gz.tbi.md5", - "full": base_name_out + ".full.vcf.gz", - "full_md5": base_name_out + ".full.vcf.gz.md5", + "full_vcf": base_name_out + ".full.vcf.gz", + "full_vcf_md5": base_name_out + ".full.vcf.gz.md5", "txt": base_name_out + ".txt", "txt_md5": base_name_out + ".txt.md5", "wig": base_name_out + ".wig", @@ -282,8 +282,8 @@ def test_mutect2_step_part_get_output_files_filter( """Tests Mutect2StepPart.get_output_files() - filter""" # Define expected expected = { - "full": mutect2_output_base_name + ".full.vcf.gz", - "full_md5": mutect2_output_base_name + ".full.vcf.gz.md5", + "full_vcf": mutect2_output_base_name + ".full.vcf.gz", + "full_vcf_md5": mutect2_output_base_name + ".full.vcf.gz.md5", "full_vcf_tbi": mutect2_output_base_name + ".full.vcf.gz.tbi", "full_vcf_tbi_md5": mutect2_output_base_name + ".full.vcf.gz.tbi.md5", "vcf": mutect2_output_base_name + ".vcf.gz", @@ -562,8 +562,8 @@ def test_strelka2_step_part_get_output_files(somatic_variant_calling_workflow): "vcf_md5": base_name_out + ".vcf.gz.md5", "vcf_tbi": base_name_out + ".vcf.gz.tbi", "vcf_tbi_md5": base_name_out + ".vcf.gz.tbi.md5", - "full": base_name_out + ".full.vcf.gz", - "full_md5": base_name_out + ".full.vcf.gz.md5", + "full_vcf": base_name_out + ".full.vcf.gz", + "full_vcf_md5": base_name_out + ".full.vcf.gz.md5", "full_vcf_tbi": base_name_out + ".full.vcf.gz.tbi", "full_vcf_tbi_md5": base_name_out + ".full.vcf.gz.tbi.md5", "stats": base_name_out + ".tsv", From 18217bc72a36b2a7dc35cecf2cc3a2d07456f836 Mon Sep 17 00:00:00 2001 From: ericblanc20 Date: Tue, 22 Aug 2023 08:57:52 +0200 Subject: [PATCH 08/19] feat: Somatic cnv checking (#426) Co-authored-by: Eric Blanc --- snappy_pipeline/apps/snappy_snake.py | 2 + .../workflows/somatic_cnv_checking/Snakefile | 129 ++++++ .../somatic_cnv_checking/__init__.py | 408 ++++++++++++++++++ .../__init__.py | 11 +- .../heterozygous_variants/environment.yaml | 1 + .../bcftools/heterozygous_variants/wrapper.py | 65 +++ .../bcftools/pileups/environment.yaml | 1 + .../wrappers/bcftools/pileups/wrapper.py | 57 +++ .../cnvkit/postprocess/environment.yaml | 1 + .../wrappers/cnvkit/postprocess/wrapper.py | 17 +- .../somatic_cnv_checking/cnv-check-plot.R | 118 +++++ .../somatic_cnv_checking/environment.yaml | 9 + .../wrappers/somatic_cnv_checking/wrapper.py | 96 +++++ .../wrappers/vcfpy/add_bed/environment.yaml | 8 + .../wrappers/vcfpy/add_bed/wrapper.py | 243 +++++++++++ .../test_workflows_somatic_cnv_checking.py | 297 +++++++++++++ ...kflows_somatic_targeted_seq_cnv_calling.py | 13 +- 17 files changed, 1467 insertions(+), 9 deletions(-) create mode 100644 snappy_pipeline/workflows/somatic_cnv_checking/Snakefile create mode 100644 snappy_pipeline/workflows/somatic_cnv_checking/__init__.py create mode 120000 snappy_wrappers/wrappers/bcftools/heterozygous_variants/environment.yaml create mode 100644 snappy_wrappers/wrappers/bcftools/heterozygous_variants/wrapper.py create mode 120000 snappy_wrappers/wrappers/bcftools/pileups/environment.yaml create mode 100644 snappy_wrappers/wrappers/bcftools/pileups/wrapper.py create mode 100644 snappy_wrappers/wrappers/somatic_cnv_checking/cnv-check-plot.R create mode 100644 snappy_wrappers/wrappers/somatic_cnv_checking/environment.yaml create mode 100644 snappy_wrappers/wrappers/somatic_cnv_checking/wrapper.py create mode 100644 snappy_wrappers/wrappers/vcfpy/add_bed/environment.yaml create mode 100644 snappy_wrappers/wrappers/vcfpy/add_bed/wrapper.py create mode 100644 tests/snappy_pipeline/workflows/test_workflows_somatic_cnv_checking.py diff --git a/snappy_pipeline/apps/snappy_snake.py b/snappy_pipeline/apps/snappy_snake.py index c47f50b94..6948b0682 100644 --- a/snappy_pipeline/apps/snappy_snake.py +++ b/snappy_pipeline/apps/snappy_snake.py @@ -31,6 +31,7 @@ ngs_sanity_checking, panel_of_normals, repeat_expansion, + somatic_cnv_checking, somatic_gene_fusion_calling, somatic_hla_loh_calling, somatic_msi_calling, @@ -86,6 +87,7 @@ "panel_of_normals": panel_of_normals, "repeat_analysis": repeat_expansion, "ngs_sanity_checking": ngs_sanity_checking, + "somatic_cnv_checking": somatic_cnv_checking, "somatic_gene_fusion_calling": somatic_gene_fusion_calling, "somatic_hla_loh_calling": somatic_hla_loh_calling, "somatic_msi_calling": somatic_msi_calling, diff --git a/snappy_pipeline/workflows/somatic_cnv_checking/Snakefile b/snappy_pipeline/workflows/somatic_cnv_checking/Snakefile new file mode 100644 index 000000000..f670a39a4 --- /dev/null +++ b/snappy_pipeline/workflows/somatic_cnv_checking/Snakefile @@ -0,0 +1,129 @@ +# -*- coding: utf-8 -*- +"""CUBI Pipeline somatic_cnv_checking step Snakefile""" + +import os + +from snappy_pipeline import expand_ref +from snappy_pipeline.workflows.somatic_cnv_checking import SomaticCnvCheckingWorkflow + +__author__ = "Eric Blanc " + +# Configuration =============================================================== + + +configfile: "config.yaml" + + +# Expand "$ref" JSON pointers in configuration (also works for YAML) +config, lookup_paths, config_paths = expand_ref("config.yaml", config) + +# WorkflowImpl Object Setup =================================================== + +wf = SomaticCnvCheckingWorkflow(workflow, config, lookup_paths, config_paths, os.getcwd()) + +# Rules ======================================================================= + + +localrules: + # Linking files from work/ to output/ should be done locally + somatic_cnv_checking_link_out_run, + + +rule all: + input: + wf.get_result_files(), + + +# House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +# Generic linking out --------------------------------------------------------- + + +rule somatic_cnv_checking_link_out_run: + input: + wf.get_input_files("link_out", "run"), + output: + wf.get_output_files("link_out", "run"), + run: + shell(wf.get_shell_cmd("link_out", "run", wildcards)) + + +# Somatic CNV Checking ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +# Run pileup to identify heterozygous variants in normal sample --------------- + + +rule somatic_cnv_checking_pileup_normal: + input: + unpack(wf.get_input_files("pileup", "normal")), + output: + **wf.get_output_files("pileup", "normal"), + threads: wf.get_resource("pileup", "normal", "threads") + resources: + time=wf.get_resource("pileup", "normal", "time"), + memory=wf.get_resource("pileup", "normal", "memory"), + partition=wf.get_resource("pileup", "normal", "partition"), + tmpdir=wf.get_resource("pileup", "normal", "tmpdir"), + log: + **wf.get_log_file("pileup", "normal"), + wrapper: + wf.wrapper_path("bcftools/heterozygous_variants") + + +# Run pileup to add read counts in the tumor sample --------------------------- + + +rule somatic_cnv_checking_pileup_tumor: + input: + unpack(wf.get_input_files("pileup", "tumor")), + output: + **wf.get_output_files("pileup", "tumor"), + threads: wf.get_resource("pileup", "tumor", "threads") + resources: + time=wf.get_resource("pileup", "tumor", "time"), + memory=wf.get_resource("pileup", "tumor", "memory"), + partition=wf.get_resource("pileup", "tumor", "partition"), + tmpdir=wf.get_resource("pileup", "tumor", "tmpdir"), + log: + **wf.get_log_file("pileup", "tumor"), + wrapper: + wf.wrapper_path("bcftools/pileups") + + +# Add CNV status at the locii ------------------------------------------------- + +if config["step_config"]["somatic_cnv_checking"]["path_cnv_calling"]: + + rule somatic_cnv_checking_cnv_run: + input: + unpack(wf.get_input_files("cnv", "run")), + output: + **wf.get_output_files("cnv", "run"), + threads: wf.get_resource("cnv", "run", "threads") + resources: + time=wf.get_resource("cnv", "run", "time"), + memory=wf.get_resource("cnv", "run", "memory"), + partition=wf.get_resource("cnv", "run", "partition"), + tmpdir=wf.get_resource("cnv", "run", "tmpdir"), + log: + **wf.get_log_file("cnv", "run"), + wrapper: + wf.wrapper_path("vcfpy/add_bed") + + # Generate report & plots ----------------------------------------------------- + + rule somatic_cnv_checking_cnv_report: + input: + unpack(wf.get_input_files("report", "run")), + output: + **wf.get_output_files("report", "run"), + threads: wf.get_resource("report", "run", "threads") + resources: + time=wf.get_resource("report", "run", "time"), + memory=wf.get_resource("report", "run", "memory"), + partition=wf.get_resource("report", "run", "partition"), + tmpdir=wf.get_resource("report", "run", "tmpdir"), + log: + **wf.get_log_file("report", "run"), + wrapper: + wf.wrapper_path("somatic_cnv_checking") diff --git a/snappy_pipeline/workflows/somatic_cnv_checking/__init__.py b/snappy_pipeline/workflows/somatic_cnv_checking/__init__.py new file mode 100644 index 000000000..f5781c417 --- /dev/null +++ b/snappy_pipeline/workflows/somatic_cnv_checking/__init__.py @@ -0,0 +1,408 @@ +# -*- coding: utf-8 -*- +"""Implementation of the ``somatic_cnv_checking`` step + +The ``somatic_cnv_checking`` step takes as the input the results of the ``ngs_mapping`` step +(aligned reads in BAM format) and performs pileups at germline locii to identify heterozygous +variants, and their B-allele frequency in the paired tumor sample. If one somatic CNV calling step +(either ``somatic_wgs_cnv_calling`` or ``somatic_targetd_seq_cnv_calling``) is present, the +log2 convarage ratio and copy number call are added to the output vcf. + +========== +Step Input +========== + +The somatic CNV checking step uses Snakemake sub workflows for using the result of the +``ngs_mapping`` step. Optionally, it can also use one Snakemake sub workflows for somatic CNV +calling, either``somatic_wgs_cnv_calling`` or ``somatic_targetd_seq_cnv_calling``. + +=========== +Step Output +=========== + +For each tumor DNA NGS library with name ``lib_name``/key ``lib_pk`` and each read mapper +``mapper`` that the library has been aligned with, and the CNV caller ``caller``, the +pipeline step will create a directory ``output/{mapper}.{caller}.{lib_name}-{lib_pk}/out`` +with symlinks of the following names to the resulting VCF, TBI, and MD5 files. + +- ``{mapper}.{var_caller}.{lib_name}-{lib_pk}.vcf.gz`` +- ``{mapper}.{var_caller}.{lib_name}-{lib_pk}.vcf.gz.tbi`` +- ``{mapper}.{var_caller}.{lib_name}-{lib_pk}.vcf.gz.md5`` +- ``{mapper}.{var_caller}.{lib_name}-{lib_pk}.vcf.gz.tbi.md5`` + +For example, it might look as follows for the example from above: + +:: + + output/ + +-- bwa.cnvkit.P001-T1-DNA1-WES1-4 + | `-- out + | |-- bwa.cnvkit.P001-T1-DNA1-WES1-4.vcf.gz + | |-- bwa.cnvkit.P001-T1-DNA1-WES1-4.vcf.gz.tbi + | |-- bwa.cnvkit.P001-T1-DNA1-WES1-4.vcf.gz.md5 + | `-- bwa.cnvkit.P001-T1-DNA1-WES1-4.vcf.gz.tbi.md5 + [...] + +===================== +Default Configuration +===================== + +The default configuration is as follows. + +.. include:: DEFAULT_CONFIG_somatic_cnv_checking.rst + +======= +Reports +======= + +Currently, no reports are generated. +""" + +import os +import sys + +from biomedsheets.shortcuts import CancerCaseSheet, CancerCaseSheetOptions, is_not_background +from snakemake.io import expand + +from snappy_pipeline.base import InvalidConfiguration +from snappy_pipeline.utils import dictify, listify +from snappy_pipeline.workflows.abstract import ( + BaseStep, + BaseStepPart, + LinkOutStepPart, + ResourceUsage, +) +from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow +from snappy_pipeline.workflows.somatic_targeted_seq_cnv_calling import ( + SomaticTargetedSeqCnvCallingWorkflow, +) +from snappy_pipeline.workflows.somatic_wgs_cnv_calling import SomaticWgsCnvCallingWorkflow + +__author__ = "Eric Blanc " + +#: Extensions of files to create as main payload +EXT_VALUES = (".vcf.gz", ".vcf.gz.tbi", ".vcf.gz.md5", ".vcf.gz.tbi.md5") + +#: Names of the files to create for the extension +EXT_NAMES = ("vcf", "vcf_tbi", "vcf_md5", "vcf_tbi_md5") + +#: Default configuration for the somatic_cnv_checking schema +DEFAULT_CONFIG = r""" +# Default configuration somatic_cnv_checking +step_config: + somatic_cnv_checking: + path_ngs_mapping: ../ngs_mapping # REQUIRED + path_cnv_calling: "" # Can use for instance ../somatic_targeted_seq_cnv_calling + cnv_assay_type: "" # Empty: no CNV, WES for somatic_targeted_seq_snv_calling step, WGS for somatic_wgs_cnv_calling step + excluded_regions: "" # Bed file of regions to be excluded + max_depth: 10000 # Max depth for pileups + min_depth: 20 # Minimum depth for reference and alternative alleles to consider variant + min_baf: 0.4 # Maximum BAF to consider variant as heterozygous (between 0 & 1/2) +""" + + +class SomaticCnvCheckingStepPart(BaseStepPart): + """Base class for CNV checking sub-steps""" + + @dictify + def _get_log_file(self, prefix): + """Return dict of log files.""" + key_ext = ( + ("log", ".log"), + ("conda_info", ".conda_info.txt"), + ("conda_list", ".conda_list.txt"), + ) + for key, ext in key_ext: + yield key, prefix + ext + yield key + "_md5", prefix + ext + ".md5" + + +class SomaticCnvCheckingPileupStepPart(SomaticCnvCheckingStepPart): + """Perform pileups at a set of locations""" + + name = "pileup" + actions = ("normal", "tumor") + + def __init__(self, parent): + super().__init__(parent) + self.ngs_mapping = self.parent.sub_workflows["ngs_mapping"] + + def get_input_files(self, action): + # Validate action + self._validate_action(action) + + def input_function_normal(wildcards): + base_path = "output/{mapper}.{library_name}/out/{mapper}.{library_name}".format( + **wildcards + ) + return { + "bam": self.ngs_mapping(base_path + ".bam"), + "bai": self.ngs_mapping(base_path + ".bam.bai"), + } + + def input_function_tumor(wildcards): + base_path = "output/{mapper}.{library_name}/out/{mapper}.{library_name}".format( + **wildcards + ) + return { + "locii": "work/{mapper}.{normal_library}/out/{mapper}.{normal_library}.normal.vcf.gz".format( + normal_library=self.parent.tumor_to_normal[wildcards.library_name], **wildcards + ), + "locii_tbi": "work/{mapper}.{normal_library}/out/{mapper}.{normal_library}.normal.vcf.gz.tbi".format( + normal_library=self.parent.tumor_to_normal[wildcards.library_name], **wildcards + ), + "bam": self.ngs_mapping(base_path + ".bam"), + "bai": self.ngs_mapping(base_path + ".bam.bai"), + } + + if action == "normal": + return input_function_normal + else: + return input_function_tumor + + def get_output_files(self, action): + """Return output files that all somatic variant calling sub steps must + return (VCF + TBI file) + """ + # Validate action + self._validate_action(action) + base_path_out = ( + "work/{{mapper}}.{{library_name}}/out/{{mapper}}.{{library_name}}.{action}{ext}" + ) + return dict(zip(EXT_NAMES, expand(base_path_out, action=action, ext=EXT_VALUES))) + + def get_log_file(self, action): + # Validate action + self._validate_action(action) + return self._get_log_file( + "work/{mapper}.{library_name}/log/{mapper}.{library_name}." + action + ) + + def get_resource_usage(self, action): + # Validate action + self._validate_action(action) + return ResourceUsage( + threads=2, + time="01:00:00" if action == "tumor" else "12:00:00", # 1 hour + memory=f"{int(3.7 * 1024 * 2)}M", + ) + + +class SomaticCnvCheckingCnvStepPart(SomaticCnvCheckingStepPart): + """Merging heterozygous variants with CNV data""" + + name = "cnv" + actions = ("run",) + + def get_input_files(self, action): + # Validate action + self._validate_action(action) + + def input_function(wildcards): + normal_library = self.parent.tumor_to_normal[wildcards.library_name] + filenames = {} + name_pattern = "{mapper}.{normal_library}" + tpl = os.path.join("work", name_pattern, "out", name_pattern + ".normal.vcf.gz") + filenames["normal"] = tpl.format(normal_library=normal_library, **wildcards) + filenames["normal_tbi"] = filenames["normal"] + ".tbi" + name_pattern = "{mapper}.{library_name}" + tpl = os.path.join("work", name_pattern, "out", name_pattern + ".tumor.vcf.gz") + filenames["tumor"] = tpl.format(**wildcards) + filenames["tumor_tbi"] = filenames["tumor"] + ".tbi" + cnv_calling = self.parent.sub_workflows["cnv_calling"] + base_path = "output/{mapper}.{caller}.{library_name}/out/{mapper}.{caller}.{library_name}".format( + **wildcards + ) + filenames["cnv"] = cnv_calling(base_path + ".bed.gz") + filenames["cnv_tbi"] = filenames["cnv"] + ".tbi" + return filenames + + return input_function + + @dictify + def get_output_files(self, action): + # Validate action + self._validate_action(action) + key_ext = {"vcf": ".vcf.gz", "tbi": ".vcf.gz.tbi"} + name_pattern = "{mapper}.{caller}.{library_name}" + key_ext["tsv"] = ".tsv" + base_path_out = "work/" + name_pattern + "/out/" + name_pattern + for key, ext in key_ext.items(): + yield (key, base_path_out + ext) + yield (key + "_md5", base_path_out + ext + ".md5") + + def get_log_file(self, action): + # Validate action + self._validate_action(action) + name_pattern = "{mapper}.{caller}.{library_name}" + return self._get_log_file(os.path.join("work", name_pattern, "log", name_pattern)) + + +class SomaticCnvCheckingReportStepPart(SomaticCnvCheckingStepPart): + """Plots of BAF vs CNV""" + + name = "report" + actions = ("run",) + + def get_input_files(self, action): + # Validate action + self._validate_action(action) + + def input_function(wildcards): + name_pattern = "{mapper}.{caller}.{library_name}".format(**wildcards) + base_path_out = "work/" + name_pattern + "/out/" + name_pattern + return {"vcf": base_path_out + ".vcf.gz", "tsv": base_path_out + ".tsv"} + + return input_function + + def get_output_files(self, action): + # Validate action + self._validate_action(action) + name_pattern = "{mapper}.{caller}.{library_name}" + base_path_out = "work/" + name_pattern + "/report/" + name_pattern + return { + "cnv": base_path_out + ".cnv.pdf", + "cnv_md5": base_path_out + ".cnv.pdf.md5", + "locus": base_path_out + ".locus.pdf", + "locus_md5": base_path_out + ".locus.pdf.md5", + "segment": base_path_out + ".segment.pdf", + "segment_md5": base_path_out + ".segment.pdf.md5", + } + + def get_log_file(self, action): + # Validate action + self._validate_action(action) + name_pattern = "{mapper}.{caller}.{library_name}" + return self._get_log_file( + os.path.join("work", name_pattern, "log", name_pattern + ".report") + ) + + +class SomaticCnvCheckingWorkflow(BaseStep): + """Perform somatic cnv checking""" + + #: Workflow name + name = "somatic_cnv_checking" + + #: Default biomed sheet class + sheet_shortcut_class = CancerCaseSheet + + sheet_shortcut_kwargs = { + "options": CancerCaseSheetOptions(allow_missing_normal=True, allow_missing_tumor=True) + } + + @classmethod + def default_config_yaml(cls): + """Return default config YAML, to be overwritten by project-specific one""" + return DEFAULT_CONFIG + + def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir): + super().__init__( + workflow, + config, + config_lookup_paths, + config_paths, + workdir, + ( + SomaticTargetedSeqCnvCallingWorkflow, + SomaticWgsCnvCallingWorkflow, + NgsMappingWorkflow, + ), + ) + if self.config["path_cnv_calling"] and self.config["cnv_assay_type"]: + if self.config["cnv_assay_type"] == "WES": + cnv_calling = "somatic_targeted_seq_cnv_calling" + elif self.config["cnv_assay_type"] == "WES": + cnv_calling = "somatic_wgs_cnv_calling" + else: + raise InvalidConfiguration( + "Illegal cnv_assay_type {}, must be either WES or WGS".format( + self.config["cnv_assay_type"] + ) + ) + self.register_sub_workflow(cnv_calling, self.config["path_cnv_calling"], "cnv_calling") + self.register_sub_workflow("ngs_mapping", self.config["path_ngs_mapping"]) + # Register sub step classes so the sub steps are available + self.register_sub_step_classes( + ( + SomaticCnvCheckingPileupStepPart, + SomaticCnvCheckingCnvStepPart, + SomaticCnvCheckingReportStepPart, + LinkOutStepPart, + ) + ) + # Assemble normal/tumor pairs + self.tumor_to_normal = {} + for sheet in filter(is_not_background, self.shortcut_sheets): + for sample_pair in sheet.all_sample_pairs: + if ( + not sample_pair.tumor_sample.dna_ngs_library + or not sample_pair.normal_sample.dna_ngs_library + ): + msg = ( + "INFO: sample pair for cancer bio sample {} has is missing primary" + "normal or primary cancer NGS library" + ) + print(msg.format(sample_pair.tumor_sample.name), file=sys.stderr) + continue + tumor_library = sample_pair.tumor_sample.dna_ngs_library.name + normal_library = sample_pair.normal_sample.dna_ngs_library.name + self.tumor_to_normal[tumor_library] = normal_library + + @listify + def get_result_files(self): + """Return list of result files for the NGS mapping workflow + + We will process all NGS libraries of all bio samples in all sample sheets. + """ + # Log files from normal pileups + name_pattern = "{mapper}.{library_name}" + chksum = ("", ".md5") + ext = ("log", "conda_info.txt", "conda_list.txt") + yield from expand( + os.path.join("output", name_pattern, "log", name_pattern + ".normal.{ext}{chksum}"), + mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], + library_name=set(self.tumor_to_normal.values()), + ext=ext, + chksum=chksum, + ) + yield from expand( + os.path.join("output", name_pattern, "log", name_pattern + ".tumor.{ext}{chksum}"), + mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], + library_name=self.tumor_to_normal.keys(), + ext=ext, + chksum=chksum, + ) + # Main result: vcf & optionally segment table if CNV available + ext = {"out": [".vcf.gz", ".vcf.gz.tbi"]} + if self.config["path_cnv_calling"]: + # CNV avaliable + name_pattern = "{mapper}.{caller}.{library_name}" + callers = self.w_config["step_config"]["somatic_targeted_seq_cnv_calling"]["tools"] + ext["out"] += [".tsv"] + ext["report"] = (".cnv.pdf", ".locus.pdf", ".segment.pdf") + ext["log"] = [ + suffix + "." + e + for suffix in ("", ".report") + for e in ("log", "conda_info.txt", "conda_list.txt") + ] + else: + name_pattern = "{mapper}.{library_name}" + callers = [] + for subdir, exts in ext.items(): + yield from expand( + os.path.join("output", name_pattern, subdir, name_pattern + "{ext}{chksum}"), + mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], + caller=callers, + library_name=self.tumor_to_normal.keys(), + ext=exts, + chksum=chksum, + ) + + def check_config(self): + """Check that the path to the NGS mapping is present""" + self.ensure_w_config( + ("step_config", "somatic_cnv_checking", "path_ngs_mapping"), + "Path to NGS mapping not configured but required for somatic variant calling", + ) + if self.config["path_cnv_calling"]: + assert self.config["cnv_assay_type"] in ("WES", "WGS") diff --git a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py index ddea1c5f7..4f80a78c5 100644 --- a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py +++ b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py @@ -621,8 +621,13 @@ def _get_output_files_call(): @staticmethod def _get_output_files_postprocess(): name_pattern = "{mapper}.cnvkit.{library_name}" - tpl = os.path.join("work", name_pattern, "out", name_pattern + ".cns") - return {"final": tpl, "final_md5": tpl + ".md5"} + tpl = os.path.join("work", name_pattern, "out", name_pattern + ".bed.gz") + return { + "final": tpl, + "final_tbi": tpl + ".tbi", + "final_md5": tpl + ".md5", + "final_tbi_md5": tpl + ".tbi.md5", + } @dictify def _get_output_files_plot(self): @@ -652,7 +657,7 @@ def _get_output_files_plot(self): @staticmethod def _get_output_files_export(): - exports = (("bed", "bed"), ("seg", "seg"), ("vcf", "vcf.gz"), ("tbi", "vcf.gz.tbi")) + exports = (("seg", "seg"), ("vcf", "vcf.gz"), ("tbi", "vcf.gz.tbi")) output_files = {} tpl = ( "work/{{mapper}}.cnvkit.{{library_name}}/out/" diff --git a/snappy_wrappers/wrappers/bcftools/heterozygous_variants/environment.yaml b/snappy_wrappers/wrappers/bcftools/heterozygous_variants/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/bcftools/heterozygous_variants/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/bcftools/heterozygous_variants/wrapper.py b/snappy_wrappers/wrappers/bcftools/heterozygous_variants/wrapper.py new file mode 100644 index 000000000..2d1770494 --- /dev/null +++ b/snappy_wrappers/wrappers/bcftools/heterozygous_variants/wrapper.py @@ -0,0 +1,65 @@ +# -*- coding: utf-8 -*- +"""Wrapper for finding heterozygous variants with bcftools +""" + +from snakemake.shell import shell + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step] + +if "args" in snakemake.params and "intervals" in snakemake.params["args"]: + locii = "-r " + snakemake.params["args"]["intervals"] +elif "locii" in snakemake.input.keys(): + locii = "-R " + snakemake.input.locii +elif "locii" in config and config["locii"]: + locii = "-R " + config["locii"] +else: + locii = "" + +# Convert minimum B-allele fraction into ratio of alternative to reference alleles +min_ratio = config["min_baf"] / (1 - config["min_baf"]) +max_ratio = 1 / min_ratio + +shell( + r""" +# ----------------------------------------------------------------------------- +# Redirect stderr to log file by default and enable printing executed commands +exec &> >(tee -a "{snakemake.log.log}") +set -x +# ----------------------------------------------------------------------------- +export TMPDIR=$(mktemp -d) +trap "rm -rf $TMPDIR" EXIT + +# Write out information about conda installation +conda list > {snakemake.log.conda_list} +conda info > {snakemake.log.conda_info} + +only_one_variant="N_ALT=2 & FORMAT/AD[:2]=0" +min_depth="FORMAT/AD[:0]>{config[min_depth]} & FORMAT/AD[:1]>{config[min_depth]}" +hetero="{min_ratio}*FORMAT/AD[:0]<=FORMAT/AD[:1] & FORMAT/AD[:1]<={max_ratio}*FORMAT/AD[:0]" + +bcftools mpileup \ + {locii} \ + --max-depth {config[max_depth]} \ + -f {snakemake.config[static_data_config][reference][path]} \ + -a "FORMAT/AD" \ + {snakemake.input.bam} \ + | bcftools filter \ + --include "$only_one_variant & $min_depth & $hetero" \ + -O z -o {snakemake.output.vcf} +tabix {snakemake.output.vcf} + +pushd $(dirname {snakemake.output.vcf}) +md5sum $(basename {snakemake.output.vcf}) > $(basename {snakemake.output.vcf_md5}) +md5sum $(basename {snakemake.output.vcf_tbi}) > $(basename {snakemake.output.vcf_tbi_md5}) +""" +) + +# Compute MD5 sums of logs +shell( + r""" +md5sum {snakemake.log.log} > {snakemake.log.log_md5} +md5sum {snakemake.log.conda_list} > {snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} > {snakemake.log.conda_info_md5} +""" +) diff --git a/snappy_wrappers/wrappers/bcftools/pileups/environment.yaml b/snappy_wrappers/wrappers/bcftools/pileups/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/bcftools/pileups/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/bcftools/pileups/wrapper.py b/snappy_wrappers/wrappers/bcftools/pileups/wrapper.py new file mode 100644 index 000000000..6c70452f2 --- /dev/null +++ b/snappy_wrappers/wrappers/bcftools/pileups/wrapper.py @@ -0,0 +1,57 @@ +# -*- coding: utf-8 -*- +"""Wrapper for running bcftools mpileup +""" + +from snakemake.shell import shell + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step] + +if "args" in snakemake.params and "intervals" in snakemake.params["args"]: + locii = "-r " + snakemake.params["args"]["intervals"] +elif "locii" in snakemake.input.keys(): + locii = "-R " + snakemake.input.locii +elif "locii" in config and config["locii"]: + locii = "-R " + config["locii"] +else: + locii = "" + +# Actually run the script. +shell( + r""" +# ----------------------------------------------------------------------------- +# Redirect stderr to log file by default and enable printing executed commands +exec &> >(tee -a "{snakemake.log.log}") +set -x +# ----------------------------------------------------------------------------- +export TMPDIR=$(mktemp -d) +trap "rm -rf $TMPDIR" EXIT + +# Write out information about conda installation +conda list > {snakemake.log.conda_list} +conda info > {snakemake.log.conda_info} + +bcftools mpileup \ + {locii} \ + --max-depth {config[max_depth]} \ + -f {snakemake.config[static_data_config][reference][path]} \ + -a "FORMAT/AD" \ + -O z -o {snakemake.output.vcf} \ + {snakemake.input.bam} +tabix {snakemake.output.vcf} + +pushd $(dirname {snakemake.output.vcf}) +md5sum $(basename {snakemake.output.vcf}) > $(basename {snakemake.output.vcf_md5}) +md5sum $(basename {snakemake.output.vcf_tbi}) > $(basename {snakemake.output.vcf_tbi_md5}) +popd +""" +) + +# Compute MD5 sums of logs +shell( + r""" +md5sum {snakemake.log.log} > {snakemake.log.log_md5} +md5sum {snakemake.log.conda_list} > {snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} > {snakemake.log.conda_info_md5} +""" +) diff --git a/snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml b/snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml index e936461b1..28ebc9a4e 100644 --- a/snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml +++ b/snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml @@ -5,3 +5,4 @@ channels: dependencies: - r-base - bioconductor-genomicranges +- htslib diff --git a/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py b/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py index f79a46585..2b35d730d 100644 --- a/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py +++ b/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py @@ -30,6 +30,8 @@ # ----------------------------------------------------------------------------- +uncompressed=$(echo "{snakemake.output.final}" | sed -e "s/\.gz$//") + cat << _EOF | R --vanilla --slave segments <- read.table("{snakemake.input.segment}", sep="\t", header=1, stringsAsFactors=FALSE) stopifnot(all(c("chromosome", "start", "end") %in% colnames(segments))) @@ -57,19 +59,30 @@ # Default value: diploid segment (number of copies = 2) segments[,"cn"] <- 2 -segments[S4Vectors::queryHits(i),"cn"] <- calls[S4Vectors::subjectHits(i),"cn"] +segments[S4Vectors::queryHits(i),"cn"] <- round(calls[S4Vectors::subjectHits(i),"cn"]) # Reset segment boundaries to original values segments[,"start"] <- segments[["start"]]-1 segments[,"end"] <- segments[["end"]]+1 -write.table(segments, file="{snakemake.output.final}", sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE) +# Create bed file (abusing name, score & strand to make it bed-6 compatible) +segments[,"start"] <- segments[["start"]]-1 # Bed files are 0-based, semi-open intervals +segments[,"name"] <- sprintf("seg_%d_cn_%d", 1:nrow(segments), segments[["cn"]]) +segments[,"score"] <- pmin(1000, abs(segments[["log2"]])) +segments[,"strand"] <- "+" +segments[segments[["log2"]]<0,"strand"] <- "-" + +write.table(segments[,c("chromosome", "start", "end", "name", "score", "strand")], file="$uncompressed", sep="\t", col.names=FALSE, row.names=FALSE, quote=FALSE) _EOF +bgzip $uncompressed +tabix {snakemake.output.final} + d=$(dirname "{snakemake.output.final}") pushd $d fn=$(basename "{snakemake.output.final}") md5sum $fn > $fn.md5 +md5sum $fn.tbi > $fn.tbi.md5 popd """ ) diff --git a/snappy_wrappers/wrappers/somatic_cnv_checking/cnv-check-plot.R b/snappy_wrappers/wrappers/somatic_cnv_checking/cnv-check-plot.R new file mode 100644 index 000000000..f6d54977e --- /dev/null +++ b/snappy_wrappers/wrappers/somatic_cnv_checking/cnv-check-plot.R @@ -0,0 +1,118 @@ +cn_to_call <- function(cn, amplification=7) { + Call <- factor(rep("Neutral", length(cn)), levels=c("Deletion", "Loss", "Neutral", "Gain", "Amplification")) + Call[!is.na(cn) & cn==0] <- "Deletion" + Call[!is.na(cn) & cn==1] <- "Loss" + Call[!is.na(cn) & 2 + dplyr::filter(!is.na(LFC) & !is.na(CN)) |> + dplyr::mutate(BAF=t_alt/(t_ref+t_alt)) |> + dplyr::mutate(Call=cn_to_call(CN)) + x +} + +cnv_to_table <- function(cnv) { + y <- read.table(cnv, sep="\t", header=0) + colnames(y) <- c("CHROM", "start", "stop", "name", "LFC", "strand") + y <- y |> + dplyr::mutate(LFC=replace(LFC, strand == "-", -abs(LFC[strand=="-"]))) |> + dplyr::mutate(start=start + 1) + y +} + +chromosome_lengths <- function(genome, use_fai=TRUE, use_dict=TRUE) { + if (use_fai && file.exists(paste(genome, "fai", sep="."))) { + genome <- read.table(paste(genome, "fai", sep="."), sep="\t", header=0) + colnames(genome) <- c("CHROM", "Length", "index", "ncol", "nbyte") + } else { + if (use_dict && file.exists(paste(genome, "dict", sep="."))) { + pattern <- "^SQ\tSN:([^ \t]+)\tLN:([0-9]+)\t.+$" + genome <- grep(pattern, readLines(paste(genome, "dict", sep=".")), value=TRUE) + genome <- data.frame(CHROM=sub(pattern, "\\1", genome), Length=as.numeric(sub(pattern, "\\2", genome))) + } else { + genome <- Biostrings::readDNAStringSet(genome) + genome <- data.frame(CHROM=names(genome), Length=Biostrings::width(genome)) + } + } + genome <- genome |> + dplyr::mutate(CHROM=sub(" .*", "", CHROM)) |> + dplyr::mutate(Offset=cumsum(as.numeric(dplyr::lag(Length, default=0)))) |> + dplyr::select(CHROM, Length, Offset) + genome +} + +default_call_colors <- c( + "Deletion"="#E41A1C", + "Loss"="#984EA3", + "Neutral"="#4DAF4A", + "Gain"="#80B1D3", + "Amplification"="#377EB8" +) + +plot_cnv <- function(x, scale=c("log2", "sqrt"), call_colors=default_call_colors) { + scale <- match.arg(scale) + if (scale == "sqrt") x_label <- "Segment Fold Change" + else x_label <- "Segment Log2 Fold Change" + if (scale == "sqrt") x <- x |> dplyr::mutate(LFC=2^LFC) + p <- x |> + dplyr::mutate(BAF=pmin(BAF, 1-BAF)) |> + ggplot2::ggplot(ggplot2::aes(x=LFC, y=BAF, color=Call)) + + ggplot2::geom_point() + + ggplot2::labs(x=x_label, y="B-allele fraction") + + ggplot2::scale_color_manual(values=call_colors) + + ggplot2::theme_bw() + if (scale == "sqrt") p <- p + ggplot2::scale_x_sqrt() + p +} + +plot_locus <- function(x, genome_lengths, call_colors=default_call_colors) { + p <- genome_lengths |> + ggplot2::ggplot(ggplot2::aes(xmin=Offset+1, xmax=Offset+Length, ymin=0, ymax=1, fill=as.character(n%%2))) + + ggplot2::geom_rect() + + ggplot2::scale_fill_manual(values=c("white", "grey")) + + ggplot2::scale_x_continuous(breaks=genome_lengths$Offset+genome_lengths$Length/2, labels=genome_lengths$CHROM) + + ggplot2::geom_point(data=x, mapping=ggplot2::aes(x=x, y=BAF, color=Call), inherit.aes=FALSE) + + ggplot2::scale_color_manual(values=call_colors) + + ggplot2::theme_bw() + + ggplot2::theme(axis.text.x=ggplot2::element_text(angle=90, vjust=0.5, hjust=1)) + + ggplot2::guides(fill="none") + + ggplot2::labs(x="Genomic position", y="B-allele fraction") + p +} + +plot_segment <- function(y, genome_lengths, call_colors=default_call_colors) { + p <- genome_lengths |> + ggplot2::ggplot(ggplot2::aes(xmin=Offset+1, xmax=Offset+Length, ymin=0, ymax=0.5, fill=as.character(n%%2))) + + ggplot2::geom_rect() + + ggplot2::scale_fill_manual(values=c("white", "grey")) + + ggplot2::scale_x_continuous(breaks=genome_lengths$Offset+genome_lengths$Length/2, labels=genome_lengths$CHROM) + p <- p + + ggplot2::geom_point(data=y, mapping=ggplot2::aes(x=(from+to)/2, y=Median, color=Call, size=Nvariants), inherit.aes=FALSE) + + ggplot2::geom_segment(data=y, mapping=ggplot2::aes(x=(from+to)/2, y=`1st quartile`, xend=(from+to)/2, yend=`3rd quartile`, color=Call), inherit.aes=FALSE) + + ggplot2::geom_segment(data=y, mapping=ggplot2::aes(x=from, y=Median, xend=to, yend=Median, color=Call), inherit.aes=FALSE) + + ggplot2::scale_color_manual(values=call_colors) + p <- p + + ggplot2::theme_bw() + + ggplot2::theme(axis.text.x=ggplot2::element_text(angle=90, vjust=0.5, hjust=1)) + + ggplot2::guides(fill="none") + + ggplot2::labs(x="Genomic position", y="B-allele fraction") + p +} diff --git a/snappy_wrappers/wrappers/somatic_cnv_checking/environment.yaml b/snappy_wrappers/wrappers/somatic_cnv_checking/environment.yaml new file mode 100644 index 000000000..6421a7e1b --- /dev/null +++ b/snappy_wrappers/wrappers/somatic_cnv_checking/environment.yaml @@ -0,0 +1,9 @@ +channels: +- conda-forge +- bioconda +dependencies: +- r-base +- r-dplyr +- r-ggplot2 +- bioconductor-variantannotation +- bioconductor-biostrings diff --git a/snappy_wrappers/wrappers/somatic_cnv_checking/wrapper.py b/snappy_wrappers/wrappers/somatic_cnv_checking/wrapper.py new file mode 100644 index 000000000..924c194e0 --- /dev/null +++ b/snappy_wrappers/wrappers/somatic_cnv_checking/wrapper.py @@ -0,0 +1,96 @@ +# -*- coding: utf-8 -*- +"""Wrapper for running CopywriteR""" + +import os + +from snakemake import shell + +__author__ = "Eric Blanc " + +shell.executable("/bin/bash") + +rscript = os.path.join(os.path.dirname(os.path.realpath(__file__)), "cnv-check-plot.R") + +reference = snakemake.config["static_data_config"]["reference"]["path"] + +shell( + r""" +set -x + +export TMPDIR=$(mktemp -d) +# trap "rm -rf $TMPDIR" EXIT + +# Also pipe stderr to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +md5() {{ + filename=$1 + fn=$(basename $filename) + pushd $(dirname $filename) 1> /dev/null 2>&1 + rslt=$(md5sum $fn) + popd 1> /dev/null 2>&1 + echo "$rslt" +}} + +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5 {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5 {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# ------------------------------------------------------------------------------------------------- +# Write helper script and call R +# +R --vanilla --slave << __EOF +source("{rscript}") + +genome_lengths <- chromosome_lengths("{reference}") |> dplyr::mutate(n=dplyr::row_number()) + +x <- vcf_to_table("{snakemake.input.vcf}", sample="{snakemake.wildcards[library_name]}") +x <- x |> dplyr::left_join(genome_lengths, by="CHROM") |> dplyr::mutate(x=POS + Offset) + +y <- read.table("{snakemake.input.tsv}", sep="\t", header=1, check.names=FALSE) +y <- y |> dplyr::mutate(Call=cn_to_call(CN)) +y <- y |> dplyr::left_join(genome_lengths, by="CHROM") |> dplyr::mutate(from=start + Offset, to=stop + Offset) + +pdf("{snakemake.output.cnv}", height=6.22, width=9.33) +plot_cnv(x, scale="log2") + ggplot2::ggtitle("{snakemake.wildcards[library_name]}") +plot_cnv(x, scale="sqrt") + ggplot2::ggtitle("{snakemake.wildcards[library_name]}") +dev.off() + +pdf("{snakemake.output.locus}", height=6.22, width=12.44) +plot_locus(x, genome_lengths |> dplyr::filter(CHROM %in% x[["CHROM"]])) + + ggplot2::ggtitle("{snakemake.wildcards[library_name]}") +dev.off() + +pdf("{snakemake.output.segment}", height=6.22, width=12.44) +plot_segment(y, genome_lengths |> dplyr::filter(CHROM %in% y[["CHROM"]])) +dev.off() +__EOF + +md5 {snakemake.output.cnv} > {snakemake.output.cnv_md5} +md5 {snakemake.output.locus} > {snakemake.output.locus_md5} +md5 {snakemake.output.segment} > {snakemake.output.segment_md5} +""" +) + +shell( + r""" +md5() {{ + filename=$1 + fn=$(basename $filename) + pushd $(dirname $filename) 1> /dev/null 2>&1 + rslt=$(md5sum $fn) + popd 1> /dev/null 2>&1 + echo "$rslt" +}} +md5 {snakemake.log.log} > {snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/vcfpy/add_bed/environment.yaml b/snappy_wrappers/wrappers/vcfpy/add_bed/environment.yaml new file mode 100644 index 000000000..8d0c6415c --- /dev/null +++ b/snappy_wrappers/wrappers/vcfpy/add_bed/environment.yaml @@ -0,0 +1,8 @@ +channels: +- conda-forge +- bioconda +dependencies: +- bcftools +- vcfpy +- pytabix +- htslib diff --git a/snappy_wrappers/wrappers/vcfpy/add_bed/wrapper.py b/snappy_wrappers/wrappers/vcfpy/add_bed/wrapper.py new file mode 100644 index 000000000..d98068a87 --- /dev/null +++ b/snappy_wrappers/wrappers/vcfpy/add_bed/wrapper.py @@ -0,0 +1,243 @@ +import math +import numbers +import re +import subprocess + +from snakemake.shell import shell +import tabix +import vcfpy + +NAME_PATTERN = re.compile("^seg_([0-9]+)_cn_([0-9]+)$") + +LFC = {"ID": "LFC", "Number": 1, "Type": "Float", "Description": "Log2 fold change from coverage"} +CN = { + "ID": "CN", + "Number": 1, + "Type": "Integer", + "Description": "Number of allele called by the CNV caller", +} + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step] + +bed = tabix.open(snakemake.input.cnv) + +ps = [] +nProc = 0 +ps += [ + subprocess.Popen( + ["bcftools", "merge", snakemake.input.normal, snakemake.input.tumor], stdout=subprocess.PIPE + ) +] +nProc += 1 +ps += [ + subprocess.Popen( + ["bcftools", "filter", "--include", "N_ALT=2 & FORMAT/AD[:2]=0"], + stdin=ps[nProc - 1].stdout, + stdout=subprocess.PIPE, + text=True, + ) +] +ps[nProc - 1].stdout.close() # Allow p1 to receive a SIGPIPE if p2 exits. +nProc += 1 +if "excluded_regions" in config and config["excluded_regions"]: + ps += [ + subprocess.Popen( + ["bcftools", "view", "--targets-file", "^" + config["excluded_regions"]], + stdin=ps[nProc - 1].stdout, + stdout=subprocess.PIPE, + text=True, + ) + ] + ps[nProc - 1].stdout.close() + nProc += 1 +reader = vcfpy.Reader.from_stream(ps[nProc - 1].stdout) + +sample = snakemake.wildcards["library_name"] +iSample = reader.header.samples.name_to_idx[sample] + +reader.header.add_format_line(LFC) +reader.header.add_format_line(CN) + +writer = vcfpy.Writer.from_path(snakemake.output.vcf, reader.header) + +segments = {} +for variant in reader: + logFoldChange = None + cn = None + + # Add default (missing) values for all samples + variant.add_format("LFC", logFoldChange) + variant.add_format("CN", cn) + + try: + locii = list(bed.query(variant.CHROM, variant.affected_start, variant.affected_end + 1)) + except tabix.TabixError as e: + print( + "Variant {}:{}{}>{} not covered by segmentation of sample {}".format( + variant.CHROM, variant.POS, variant.REF, variant.ALT[0].value, sample + ) + ) + continue + + if len(locii) == 0: + print( + "Variant {}:{}{}>{} not covered by segmentation of sample {}".format( + variant.CHROM, variant.POS, variant.REF, variant.ALT[0].value, sample + ) + ) + elif len(locii) == 1: + for locus in locii: + logFoldChange = float(locus[4]) + if locus[5] == "-": + logFoldChange = -logFoldChange + m = NAME_PATTERN.match(locus[3]) + assert m + cn = int(m.groups()[1]) + else: + print( + "Variant {}:{}{}>{} crosses segments in sample {}".format( + variant.CHROM, variant.POS, variant.REF, variant.ALT[0].value, sample + ) + ) + for locus in locii: + m = NAME_PATTERN.match(locus[3]) + assert m + if cn is None: + cn = int(m.groups()[1]) + else: + if cn != int(m.groups()[1]): + cn = None + break + + variant.calls[iSample].data["LFC"] = logFoldChange + variant.calls[iSample].data["CN"] = cn + + writer.write_record(variant) + + if len(locii) == 1: + locus = locii[0] + if locus[3] not in segments: + segments[locus[3]] = { + "logFoldChange": logFoldChange, + "CHROM": locus[0], + "start": locus[1], + "stop": locus[2], + "BAFs": [], + "NoData": 0, + } + depth = variant.call_for_sample[sample].data["AD"] + if len(depth) == 0: + segments[locus[3]]["NoData"] += 1 + else: + if depth[0] is None: + depth[0] = 0 + if depth[1] is None: + depth[1] = 0 + if depth[0] + depth[1] == 0: + segments[locus[3]]["NoData"] += 1 + else: + baf = min(depth[0], depth[1]) / (depth[0] + depth[1]) + segments[locus[3]]["BAFs"] += [baf] + +writer.close() + +# Implmentation of R's quantile function for continuous quantiles. +def quantile(x, probs, na_rm=False, method=7): + if na_rm: + x = list( + filter( + lambda y: y is not None + and isinstance(y, Number) + and not math.isnan(y) + and not math.isinf(y), + x, + ) + ) + x.sort() + n = len(x) + if method == 4: + m = [0 for p in probs] + elif method == 5: + m = [0.5 for p in probs] + elif method == 6: + m = [p for p in probs] + elif method == 7: + m = [1 - p for p in probs] + elif method == 8: + m = [(p + 1) / 3 for p in probs] + elif method == 9: + m = [p / 4 + 3 / 8 for p in probs] + else: + raise NotImplementedError("Only continuous methods 4 to 9 (R) are implmented") + qs = [None] * len(probs) + for i in range(len(probs)): + j = math.floor(n * probs[i] + m[i]) + if j < 1: + qs[i] = x[j] + elif j >= n: + qs[i] = x[n - 1] + else: + g = n * probs[i] + m[i] - j + qs[i] = (1 - g) * x[j - 1] + g * x[j] + return qs + + +with open(snakemake.output.tsv, "wt") as f: + print( + "Number\tCHROM\tstart\tstop\tCN\tLFC\tNvariants\tMin\t1st quartile\tMedian\t3rd quartile\tMax\tNoData", + file=f, + ) + for segId, segment in segments.items(): + m = NAME_PATTERN.match(segId) + n = int(m.groups()[0]) + cn = int(m.groups()[1]) + + logFoldChange = segment["logFoldChange"] + nVar = len(segment["BAFs"]) + bafs = sorted(segment["BAFs"]) + + if nVar > 1: + qs = ( + [bafs[0]] + + quantile(segment["BAFs"], (0.25, 0.5, 0.75), method=8) + + [bafs[nVar - 1]] + ) + elif nVar == 1: + qs = [bafs[0]] * 5 + else: + qs = [""] * 5 + + values = ( + [ + n, + segment["CHROM"], + segment["start"], + segment["stop"], + cn, + segment["logFoldChange"], + nVar, + ] + + qs + + [segment["NoData"]] + ) + print("\t".join(map(str, values)), file=f) + +shell( + r""" +tabix {snakemake.output.vcf} + +md5() {{ + filename=$1 + fn=$(basename $filename) + pushd $(dirname $filename) 1> /dev/null 2>&1 + rslt=$(md5sum $fn) + popd 1> /dev/null 2>&1 + echo "$rslt" +}} + +md5 {snakemake.output.vcf} > {snakemake.output.vcf_md5} +md5 {snakemake.output.tbi} > {snakemake.output.tbi_md5} +md5 {snakemake.output.tsv} > {snakemake.output.tsv_md5} +""" +) diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_cnv_checking.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_cnv_checking.py new file mode 100644 index 000000000..2310f7676 --- /dev/null +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_cnv_checking.py @@ -0,0 +1,297 @@ +# -*- coding: utf-8 -*- +"""Tests for the somatic_cnv_checking workflow module code""" + + +import textwrap + +import pytest +import ruamel.yaml as ruamel_yaml +from snakemake.io import Wildcards + +from snappy_pipeline.workflows.somatic_cnv_checking import SomaticCnvCheckingWorkflow + +from .common import get_expected_log_files_dict, get_expected_output_vcf_files_dict +from .conftest import patch_module_fs + +__author__ = "Manuel Holtgrewe " + + +@pytest.fixture(scope="module") # otherwise: performance issues +def minimal_config(): + """Return YAML parsing result for (somatic) configuration""" + yaml = ruamel_yaml.YAML() + return yaml.load( + textwrap.dedent( + r""" + static_data_config: + reference: + path: /path/to/ref.fa + dbsnp: + path: /path/to/dbsnp.vcf.gz + + step_config: + ngs_mapping: + tools: + dna: ['bwa'] + + somatic_targeted_seq_cnv_calling: + tools: ["cnvkit"] + + somatic_cnv_checking: + path_ngs_mapping: ../ngs_mapping + path_cnv_calling: ../somatic_targeted_seq_cnv_calling + cnv_assay_type: WES + + data_sets: + first_batch: + file: sheet.tsv + search_patterns: + - {'left': '*/*/*_R1.fastq.gz', 'right': '*/*/*_R2.fastq.gz'} + search_paths: ['/path'] + type: matched_cancer + naming_scheme: only_secondary_id + """ + ).lstrip() + ) + + +@pytest.fixture +def somatic_cnv_checking_workflow( + dummy_workflow, + minimal_config, + config_lookup_paths, + work_dir, + config_paths, + cancer_sheet_fake_fs, + mocker, +): + """Return SomaticTargetedSeqCnvCallingWorkflow object pre-configured with germline sheet""" + # Patch out file-system related things in abstract (the crawling link in step is defined there) + patch_module_fs("snappy_pipeline.workflows.abstract", cancer_sheet_fake_fs, mocker) + # Update the "globals" attribute of the mock workflow (snakemake.workflow.Workflow) so we + # can obtain paths from the function as if we really had a NGSMappingPipelineStep here + dummy_workflow.globals = { + "ngs_mapping": lambda x: "NGS_MAPPING/" + x, + "cnv_calling": lambda x: "CNV_CALLING/" + x, + } + # Construct the workflow object + return SomaticCnvCheckingWorkflow( + dummy_workflow, + minimal_config, + config_lookup_paths, + config_paths, + work_dir, + ) + + +# Tests for CnvCheckingPileupStepPart -------------------------------------------------------------- + + +def test_pileup_normal_step_part_get_input_files(somatic_cnv_checking_workflow): + """Tests CnvCheckingPileupStepPart.get_input_files() - action normal""" + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-N1-DNA1-WGS1"}) + expected = { + "bam": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam", + "bai": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam.bai", + } + actual = somatic_cnv_checking_workflow.get_input_files("pileup", "normal")(wildcards) + assert actual == expected + + +def test_pileup_normal_step_part_get_output_files(somatic_cnv_checking_workflow): + """Tests CnvCheckingPileupStepPart.get_output_files() - action normal""" + base_name = "work/{mapper}.{library_name}/out/{mapper}.{library_name}.normal" + expected = get_expected_output_vcf_files_dict(base_out=base_name) + actual = somatic_cnv_checking_workflow.get_output_files("pileup", "normal") + assert actual == expected + + +def test_pileup_normal_step_part_get_log_file(somatic_cnv_checking_workflow): + """Tests CnvCheckingPileupStepPart.get_log_file() - action normal""" + base_name = "work/{mapper}.{library_name}/log/{mapper}.{library_name}.normal" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_cnv_checking_workflow.get_log_file("pileup", "normal") + assert actual == expected + + +def test_pileup_normal_step_part_get_resource(somatic_cnv_checking_workflow): + """Tests CnvCheckingPileupStepPart.get_resource() - action normal""" + expected_dict = {"threads": 2, "time": "12:00:00", "memory": "7577M", "partition": "medium"} + for resource, expected in expected_dict.items(): + msg_error = f"Assertion error for resource '{resource}'." + actual = somatic_cnv_checking_workflow.get_resource("pileup", "normal", resource) + assert actual == expected, msg_error + + +def test_pileup_tumor_step_part_get_input_files(somatic_cnv_checking_workflow): + """Tests CnvCheckingPileupStepPart.get_input_files() - action tumor""" + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) + expected = { + "locii": "work/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.normal.vcf.gz", + "locii_tbi": "work/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.normal.vcf.gz.tbi", + "bam": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam", + "bai": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam.bai", + } + actual = somatic_cnv_checking_workflow.get_input_files("pileup", "tumor")(wildcards) + assert actual == expected + + +def test_pileup_tumor_step_part_get_output_files(somatic_cnv_checking_workflow): + """Tests CnvCheckingPileupStepPart.get_output_files() - action tumor""" + base_name = "work/{mapper}.{library_name}/out/{mapper}.{library_name}.tumor" + expected = get_expected_output_vcf_files_dict(base_out=base_name) + actual = somatic_cnv_checking_workflow.get_output_files("pileup", "tumor") + assert actual == expected + + +def test_pileup_tumor_step_part_get_log_file(somatic_cnv_checking_workflow): + """Tests CnvCheckingPileupStepPart.get_log_file() - action tumor""" + base_name = "work/{mapper}.{library_name}/log/{mapper}.{library_name}.tumor" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_cnv_checking_workflow.get_log_file("pileup", "tumor") + assert actual == expected + + +def test_pileup_tumor_step_part_get_resource(somatic_cnv_checking_workflow): + """Tests CnvCheckingPileupStepPart.get_resource() - action tumor""" + expected_dict = {"threads": 2, "time": "01:00:00", "memory": "7577M", "partition": "medium"} + for resource, expected in expected_dict.items(): + msg_error = f"Assertion error for resource '{resource}'." + actual = somatic_cnv_checking_workflow.get_resource("pileup", "tumor", resource) + assert actual == expected, msg_error + + +def test_cnv_run_step_part_get_input_files(somatic_cnv_checking_workflow): + """Tests SomaticCnvCheckingCnvStepPart.get_input_files()""" + wildcards = Wildcards( + fromdict={"mapper": "bwa", "caller": "cnvkit", "library_name": "P001-T1-DNA1-WGS1"} + ) + expected = { + "cnv": "CNV_CALLING/output/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.bed.gz", + "cnv_tbi": "CNV_CALLING/output/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.bed.gz.tbi", + "normal": "work/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.normal.vcf.gz", + "normal_tbi": "work/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.normal.vcf.gz.tbi", + "tumor": "work/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.tumor.vcf.gz", + "tumor_tbi": "work/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.tumor.vcf.gz.tbi", + } + actual = somatic_cnv_checking_workflow.get_input_files("cnv", "run")(wildcards) + assert actual == expected + + +def test_cnv_run_step_part_get_output_files(somatic_cnv_checking_workflow): + """Tests SomaticCnvCheckingCnvStepPart.get_output_files()""" + base_name = "work/{mapper}.{caller}.{library_name}/out/{mapper}.{caller}.{library_name}" + expected = { + "vcf": base_name + ".vcf.gz", + "vcf_md5": base_name + ".vcf.gz.md5", + "tbi": base_name + ".vcf.gz.tbi", + "tbi_md5": base_name + ".vcf.gz.tbi.md5", + "tsv": base_name + ".tsv", + "tsv_md5": base_name + ".tsv.md5", + } + actual = somatic_cnv_checking_workflow.get_output_files("cnv", "run") + assert actual == expected + + +def test_cnv_run_step_part_get_log_file(somatic_cnv_checking_workflow): + """Tests SomaticCnvCheckingCnvStepPart.get_log_file()""" + base_name = "work/{mapper}.{caller}.{library_name}/log/{mapper}.{caller}.{library_name}" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_cnv_checking_workflow.get_log_file("cnv", "run") + assert actual == expected + + +def test_report_run_step_part_get_input_files(somatic_cnv_checking_workflow): + """Tests SomaticCnvCheckingReportStepPart.get_input_files()""" + wildcards = Wildcards( + fromdict={"mapper": "bwa", "caller": "cnvkit", "library_name": "P001-T1-DNA1-WGS1"} + ) + expected = { + "vcf": "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.vcf.gz", + "tsv": "work/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.tsv", + } + actual = somatic_cnv_checking_workflow.get_input_files("report", "run")(wildcards) + assert actual == expected + + +def test_report_run_step_part_get_output_files(somatic_cnv_checking_workflow): + """Tests SomaticCnvCheckingReportStepPart.get_output_files()""" + base_name = "work/{mapper}.{caller}.{library_name}/report/{mapper}.{caller}.{library_name}" + expected = { + "cnv": base_name + ".cnv.pdf", + "cnv_md5": base_name + ".cnv.pdf.md5", + "locus": base_name + ".locus.pdf", + "locus_md5": base_name + ".locus.pdf.md5", + "segment": base_name + ".segment.pdf", + "segment_md5": base_name + ".segment.pdf.md5", + } + actual = somatic_cnv_checking_workflow.get_output_files("report", "run") + assert actual == expected + + +def test_report_run_step_part_get_log_file(somatic_cnv_checking_workflow): + """Tests SomaticCnvCheckingReportStepPart.get_log_file()""" + base_name = "work/{mapper}.{caller}.{library_name}/log/{mapper}.{caller}.{library_name}.report" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_cnv_checking_workflow.get_log_file("report", "run") + assert actual == expected + + +# Tests for SomaticCnvCheckingWorkflow -------------------------------------------------- + + +def test_somatic_cnv_checking_workflow(somatic_cnv_checking_workflow): + """Test simple functionality of the workflow""" + # Check created sub steps + expected = ["cnv", "link_out", "pileup", "report"] + actual = list(sorted(somatic_cnv_checking_workflow.sub_steps.keys())) + assert actual == expected + + # main output + tpl = ( + "output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/out/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.{ext}{chksum}" + ) + expected = [ + tpl.format(i=i, t=t, ext=ext, chksum=chksum) + for i, t in ((1, 1), (2, 1), (2, 2)) + for ext in ("vcf.gz", "vcf.gz.tbi", "tsv") + for chksum in ("", ".md5") + ] + + # report + tpl = "output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/report/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.{ext}{chksum}" + expected += [ + tpl.format(i=i, t=t, ext=ext, chksum=chksum) + for i, t in ((1, 1), (2, 1), (2, 2)) + for ext in ("cnv.pdf", "locus.pdf", "segment.pdf") + for chksum in ("", ".md5") + ] + + # logs (no caller) + tpl = "output/bwa.P00{i}-N1-DNA1-WGS1/log/bwa.P00{i}-N1-DNA1-WGS1.normal.{ext}{chksum}" + expected += [ + tpl.format(i=i, ext=ext, chksum=chksum) + for i in (1, 2) + for ext in ("log", "conda_info.txt", "conda_list.txt") + for chksum in ("", ".md5") + ] + tpl = "output/bwa.P00{i}-T{t}-DNA1-WGS1/log/bwa.P00{i}-T{t}-DNA1-WGS1.tumor.{ext}{chksum}" + expected += [ + tpl.format(i=i, t=t, ext=ext, chksum=chksum) + for i, t in ((1, 1), (2, 1), (2, 2)) + for ext in ("log", "conda_info.txt", "conda_list.txt") + for chksum in ("", ".md5") + ] + # logs (with caller) + tpl = "output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/log/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1{part}.{ext}{chksum}" + expected += [ + tpl.format(i=i, t=t, part=part, ext=ext, chksum=chksum) + for i, t in ((1, 1), (2, 1), (2, 2)) + for part in ("", ".report") + for ext in ("log", "conda_info.txt", "conda_list.txt") + for chksum in ("", ".md5") + ] + + expected = list(sorted(expected)) + actual = list(sorted(somatic_cnv_checking_workflow.get_result_files())) + assert expected == actual diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py index fd756d9a4..ff622624c 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py @@ -472,8 +472,13 @@ def test_cnvkit_postprocess_step_part_get_input_files(somatic_targeted_seq_cnv_c def test_cnvkit_postprocess_step_part_get_output_files(somatic_targeted_seq_cnv_calling_workflow): - base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.cns" - expected = {"final": base_name_out, "final_md5": base_name_out + ".md5"} + base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.bed.gz" + expected = { + "final": base_name_out, + "final_tbi": base_name_out + ".tbi", + "final_md5": base_name_out + ".md5", + "final_tbi_md5": base_name_out + ".tbi.md5", + } actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("cnvkit", "postprocess") assert actual == expected @@ -582,7 +587,7 @@ def test_cnvkit_export_step_part_get_output_files(somatic_targeted_seq_cnv_calli # Define expected expected = {} base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}" - for key, ext in (("bed", "bed"), ("seg", "seg"), ("vcf", "vcf.gz"), ("tbi", "vcf.gz.tbi")): + for key, ext in (("seg", "seg"), ("vcf", "vcf.gz"), ("tbi", "vcf.gz.tbi")): expected[key] = base_name_out + "." + ext expected[key + "_md5"] = expected[key] + ".md5" # Get actual @@ -870,7 +875,7 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call expected += [ tpl.format(i=i, t=t, ext=ext, md5=md5) for i, t in ((1, 1), (2, 1), (2, 2)) - for ext in ("cnr", "cns", "bed", "seg", "vcf.gz", "vcf.gz.tbi") + for ext in ("cnr", "bed.gz", "bed.gz.tbi", "seg", "vcf.gz", "vcf.gz.tbi") for md5 in ("", ".md5") ] tpl = ( From c5f9dde2d2ce8570779030c1917b3132918ad33b Mon Sep 17 00:00:00 2001 From: ericblanc20 Date: Tue, 22 Aug 2023 13:50:40 +0200 Subject: [PATCH 09/19] feat: Added support for scarHRD (#429) --- snappy_pipeline/apps/snappy_snake.py | 4 +- .../Snakefile | 105 ++++++ .../__init__.py | 300 ++++++++++++++++++ .../wrappers/scarHRD/environment.yaml | 10 + .../scarHRD/gcreference/environment.yaml | 1 + .../wrappers/scarHRD/gcreference/wrapper.py | 49 +++ .../wrappers/scarHRD/install/environment.yaml | 1 + .../wrappers/scarHRD/install/wrapper.py | 48 +++ .../wrappers/scarHRD/run/environment.yaml | 1 + .../wrappers/scarHRD/run/wrapper.py | 81 +++++ ...ows_homologous_recombination_deficiency.py | 200 ++++++++++++ 11 files changed, 798 insertions(+), 2 deletions(-) create mode 100644 snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile create mode 100644 snappy_pipeline/workflows/homologous_recombination_deficiency/__init__.py create mode 100644 snappy_wrappers/wrappers/scarHRD/environment.yaml create mode 120000 snappy_wrappers/wrappers/scarHRD/gcreference/environment.yaml create mode 100644 snappy_wrappers/wrappers/scarHRD/gcreference/wrapper.py create mode 120000 snappy_wrappers/wrappers/scarHRD/install/environment.yaml create mode 100644 snappy_wrappers/wrappers/scarHRD/install/wrapper.py create mode 120000 snappy_wrappers/wrappers/scarHRD/run/environment.yaml create mode 100644 snappy_wrappers/wrappers/scarHRD/run/wrapper.py create mode 100644 tests/snappy_pipeline/workflows/test_workflows_homologous_recombination_deficiency.py diff --git a/snappy_pipeline/apps/snappy_snake.py b/snappy_pipeline/apps/snappy_snake.py index 6948b0682..d6ea062f3 100644 --- a/snappy_pipeline/apps/snappy_snake.py +++ b/snappy_pipeline/apps/snappy_snake.py @@ -25,13 +25,13 @@ helper_gcnv_model_targeted, helper_gcnv_model_wgs, hla_typing, + homologous_recombination_deficiency, igv_session_generation, ngs_data_qc, ngs_mapping, ngs_sanity_checking, panel_of_normals, repeat_expansion, - somatic_cnv_checking, somatic_gene_fusion_calling, somatic_hla_loh_calling, somatic_msi_calling, @@ -81,13 +81,13 @@ "helper_gcnv_model_targeted": helper_gcnv_model_targeted, "helper_gcnv_model_wgs": helper_gcnv_model_wgs, "hla_typing": hla_typing, + "homologous_recombination_deficiency": homologous_recombination_deficiency, "igv_session_generation": igv_session_generation, "ngs_mapping": ngs_mapping, "ngs_data_qc": ngs_data_qc, "panel_of_normals": panel_of_normals, "repeat_analysis": repeat_expansion, "ngs_sanity_checking": ngs_sanity_checking, - "somatic_cnv_checking": somatic_cnv_checking, "somatic_gene_fusion_calling": somatic_gene_fusion_calling, "somatic_hla_loh_calling": somatic_hla_loh_calling, "somatic_msi_calling": somatic_msi_calling, diff --git a/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile b/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile new file mode 100644 index 000000000..92f92482d --- /dev/null +++ b/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile @@ -0,0 +1,105 @@ +# -*- coding: utf-8 -*- +"""CUBI Pipeline homologous_recombination_deficiency step Snakefile""" + +import os + +from snappy_pipeline import expand_ref +from snappy_pipeline.workflows.homologous_recombination_deficiency import ( + HomologousRecombinationDeficiencyWorkflow, +) + +__author__ = "Eric Blanc" + + +# Configuration =============================================================== + + +configfile: "config.yaml" + + +# Expand "$ref" JSON pointers in configuration (also works for YAML) +config, lookup_paths, config_paths = expand_ref("config.yaml", config) + +# WorkflowImpl Object Setup =================================================== + +wf = HomologousRecombinationDeficiencyWorkflow( + workflow, config, lookup_paths, config_paths, os.getcwd() +) + +# Rules ======================================================================= + + +localrules: + # Linking files from work/ to output/ should be done locally + homologous_recombination_deficiency_link_out_run, + + +rule all: + input: + wf.get_result_files(), + + +# House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +# Generic linking out --------------------------------------------------------- + + +rule homologous_recombination_deficiency_link_out_run: + input: + wf.get_input_files("link_out", "run"), + output: + wf.get_output_files("link_out", "run"), + run: + shell(wf.get_shell_cmd("link_out", "run", wildcards)) + + +# Homologous Recombination Deficiency score ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +# Run scarHRD ----------------------------------------------------------------- + + +rule homologous_recombination_deficiency_scarHRD_install: + output: + **wf.get_output_files("scarHRD", "install"), + threads: wf.get_resource("scarHRD", "install", "threads") + resources: + time=wf.get_resource("scarHRD", "install", "time"), + memory=wf.get_resource("scarHRD", "install", "memory"), + partition=wf.get_resource("scarHRD", "install", "partition"), + tmpdir=wf.get_resource("scarHRD", "install", "tmpdir"), + log: + **wf.get_log_file("scarHRD", "install"), + wrapper: + wf.wrapper_path("scarHRD/install") + + +rule homologous_recombination_deficiency_scarHRD_gcreference: + output: + **wf.get_output_files("scarHRD", "gcreference"), + threads: wf.get_resource("scarHRD", "gcreference", "threads") + resources: + time=wf.get_resource("scarHRD", "gcreference", "time"), + memory=wf.get_resource("scarHRD", "gcreference", "memory"), + partition=wf.get_resource("scarHRD", "gcreference", "partition"), + tmpdir=wf.get_resource("scarHRD", "gcreference", "tmpdir"), + log: + **wf.get_log_file("scarHRD", "gcreference"), + wrapper: + wf.wrapper_path("scarHRD/gcreference") + + +rule homologous_recombination_deficiency_scarHRD_run: + input: + unpack(wf.get_input_files("scarHRD", "run")), + output: + **wf.get_output_files("scarHRD", "run"), + threads: wf.get_resource("scarHRD", "run", "threads") + resources: + time=wf.get_resource("scarHRD", "run", "time"), + memory=wf.get_resource("scarHRD", "run", "memory"), + partition=wf.get_resource("scarHRD", "run", "partition"), + tmpdir=wf.get_resource("scarHRD", "run", "tmpdir"), + log: + **wf.get_log_file("scarHRD", "run"), + wrapper: + wf.wrapper_path("scarHRD/run") diff --git a/snappy_pipeline/workflows/homologous_recombination_deficiency/__init__.py b/snappy_pipeline/workflows/homologous_recombination_deficiency/__init__.py new file mode 100644 index 000000000..bae0d34c6 --- /dev/null +++ b/snappy_pipeline/workflows/homologous_recombination_deficiency/__init__.py @@ -0,0 +1,300 @@ +# -*- coding: utf-8 -*- +"""Implementation of the ``homologous_recombination_deficiency`` step + +This step allows for the computation of the scarHRD score, which is a composite of +loss-of-heterozygocity, large-scale transitions and telomeric imbalances. +The score is a proxy for holomogous recombination deficiencies scores produced from SNP arrays. +The software is described in `Sztupinszki et al.`, +but it is not part of CRAN, Bioconductor or bioconda (currently). +The implementation also relies on versions of `sequenza` & +`copynumber` which are not part of CRAN or Bioconductor anymore. +The most recent version of sequanza is downloaded from anaconda (for the R scripts), +and from bioconda for the python utilities. Note that anaconda lists the r-sequenza package in the +bioconda directory, while this package is not found when searching `bioconda`. +copynumber is obtained from a fork of the official Bioconductor deprecated package. + +========== +Step Input +========== + +``homologous_recombination_deficiency`` starts off the aligned reads, i.e. ``ngs_mapping``. +Both the normal & tumor samples are required to generate the score. + +=========== +Step Output +=========== + +Generally, the following links are generated to ``output/``. + +.. note:: Tool-Specific Output + + As the only integrated tool is scarHRD at the moment, the output is very tailored to the result + of this tool. In the future, this section might contain "common" output and tool-specific + output sub sections. + +- ``{mapper}.scarHRD.{lib_name}-{lib_pk}/out/`` + - ``{mapper}.scarHRD.{lib_name}-{lib_pk}.seqz.gz`` + - ``{mapper}.scarHRD.{lib_name}-{lib_pk}.json`` + +===================== +Default Configuration +===================== + +The default configuration is as follows. + +.. include:: DEFAULT_CONFIG_homologous_recombination_deficiency.rst + +===================================== +Available HRD tools +===================================== + +- ``scarHRD`` + +""" + +from collections import OrderedDict +import sys + +from biomedsheets.shortcuts import CancerCaseSheet, is_not_background +from snakemake.io import expand + +from snappy_pipeline.base import UnsupportedActionException +from snappy_pipeline.utils import dictify, listify +from snappy_pipeline.workflows.abstract import ( + BaseStep, + BaseStepPart, + LinkOutStepPart, + ResourceUsage, +) +from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow + +__author__ = "Eric Blanc " + +#: Default configuration for the homologous recombination deficiency step +DEFAULT_CONFIG = r""" +# Default configuration homologous_recombination_deficiency +step_config: + homologous_recombination_deficiency: + tools: ['scarHRD'] # REQUIRED - available: 'mantis' + path_ngs_mapping: ../ngs_mapping # REQUIRED + scarHRD: + genome_name: "grch37" # Must be either "grch37", "grch38" or "mouse" + chr_prefix: False + length: 50 # Wiggle track for GC reference file +""" + + +class ScarHRDStepPart(BaseStepPart): + """Computes homologous recombination deficiency score with scarHRD""" + + #: Step name + name = "scarHRD" + + #: Class available actions + actions = ( + "install", + "gcreference", + "run", + ) + + def __init__(self, parent): + super().__init__(parent) + self.base_path_out = ( + "work/{{mapper}}.scarHRD.{{library_name}}/out/{{mapper}}.scarHRD.{{library_name}}{ext}" + ) + # Build shortcut from cancer bio sample name to matched cancer sample + self.tumor_ngs_library_to_sample_pair = OrderedDict() + for sheet in self.parent.shortcut_sheets: + self.tumor_ngs_library_to_sample_pair.update( + sheet.all_sample_pairs_by_tumor_dna_ngs_library + ) + + def get_normal_lib_name(self, wildcards): + """Return name of normal (non-cancer) library""" + pair = self.tumor_ngs_library_to_sample_pair[wildcards.library_name] + return pair.normal_sample.dna_ngs_library.name + + def get_input_files(self, action): + def input_function_run(wildcards): + """Helper wrapper function""" + # Get shorcut to Snakemake sub workflow + ngs_mapping = self.parent.sub_workflows["ngs_mapping"] + # Get names of primary libraries of the selected cancer bio sample and the + # corresponding primary normal sample + normal_base_path = ( + "output/{mapper}.{normal_library}/out/{mapper}.{normal_library}".format( + normal_library=self.get_normal_lib_name(wildcards), **wildcards + ) + ) + tumor_base_path = ( + "output/{mapper}.{library_name}/out/" "{mapper}.{library_name}" + ).format(**wildcards) + return { + "lib_path": "work/R_packages/out/.done", + "gc": "work/static_data/out/{genome_name}_{length}.wig.gz".format( + genome_name=self.config["scarHRD"]["genome_name"], + length=self.config["scarHRD"]["length"], + ), + "normal_bam": ngs_mapping(normal_base_path + ".bam"), + "normal_bai": ngs_mapping(normal_base_path + ".bam.bai"), + "tumor_bam": ngs_mapping(tumor_base_path + ".bam"), + "tumor_bai": ngs_mapping(tumor_base_path + ".bam.bai"), + } + + if action == "install": + return None + elif action == "gcreference": + return None + elif action == "run": + return input_function_run + else: + raise UnsupportedActionException( + "Action '{action}' is not supported. Valid options: {valid}".format( + action=action, valid=", ".join(self.actions) + ) + ) + + def get_output_files(self, action): + if action == "install": + return {"lib_path": "work/R_packages/out/.done"} + elif action == "gcreference": + return { + "gc": "work/static_data/out/{genome_name}_{length}.wig.gz".format( + genome_name=self.config["scarHRD"]["genome_name"], + length=self.config["scarHRD"]["length"], + ) + } + elif action == "run": + return { + "sequenza": "work/{mapper}.scarHRD.{library_name}/out/{mapper}.scarHRD.{library_name}.seqz.gz", + "scarHRD": "work/{mapper}.scarHRD.{library_name}/out/{mapper}.scarHRD.{library_name}.json", + } + else: + raise UnsupportedActionException( + "Action '{action}' is not supported. Valid options: {valid}".format( + action=action, valid=", ".join(self.actions) + ) + ) + + @dictify + def _get_log_file(self, action): + """Return dict of log files.""" + if action == "install": + prefix = "work/R_packages/log/R_packages" + elif action == "gcreference": + prefix = "work/static_data/log/{genome_name}_{length}".format( + genome_name=self.config["scarHRD"]["genome_name"], + length=self.config["scarHRD"]["length"], + ) + elif action == "run": + prefix = "work/{mapper}.scarHRD.{library_name}/log/{mapper}.scarHRD.{library_name}" + else: + raise UnsupportedActionException( + "Action '{action}' is not supported. Valid options: {valid}".format( + action=action, valid=", ".join(self.actions) + ) + ) + key_ext = ( + ("log", ".log"), + ("conda_info", ".conda_info.txt"), + ("conda_list", ".conda_list.txt"), + ) + for key, ext in key_ext: + yield key, prefix + ext + yield key + "_md5", prefix + ext + ".md5" + + def get_resource_usage(self, action): + """Get Resource Usage + + :param action: Action (i.e., step) in the workflow, example: 'run'. + :type action: str + + :return: Returns ResourceUsage for step. + """ + if action == "install" or action == "gcreference": + return ResourceUsage( + threads=1, + time="02:00:00", # 2 hours + memory="4096M", + partition="short", + ) + elif action == "run": + return ResourceUsage( + threads=2, + time="48:00:00", # 2 hours + memory="32G", + ) + else: + raise UnsupportedActionException( + "Action '{action}' is not supported. Valid options: {valid}".format( + action=action, valid=", ".join(self.actions) + ) + ) + + +class HomologousRecombinationDeficiencyWorkflow(BaseStep): + """Compute Homologous Recombination Deficiency score""" + + #: Step name + name = "homologous_recombination_deficiency" + + #: Default biomed sheet class + sheet_shortcut_class = CancerCaseSheet + + @classmethod + def default_config_yaml(cls): + """Return default config YAML, to be overwritten by project-specific one""" + return DEFAULT_CONFIG + + def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir): + super().__init__( + workflow, + config, + config_lookup_paths, + config_paths, + workdir, + (NgsMappingWorkflow,), + ) + # Register sub step classes so the sub steps are available + self.register_sub_step_classes((ScarHRDStepPart, LinkOutStepPart)) + # Initialize sub-workflows + self.register_sub_workflow("ngs_mapping", self.config["path_ngs_mapping"]) + + @listify + def get_result_files(self): + """Return list of result files for the somatic targeted sequencing CNV calling step""" + tool_actions = {"scarHRD": ("run",)} + for sheet in filter(is_not_background, self.shortcut_sheets): + for sample_pair in sheet.all_sample_pairs: + if ( + not sample_pair.tumor_sample.dna_ngs_library + or not sample_pair.normal_sample.dna_ngs_library + ): + msg = ( + "INFO: sample pair for cancer bio sample {} is missing primary" + "normal or primary cancer NGS library" + ) + print(msg.format(sample_pair.tumor_sample.name), file=sys.stderr) + continue + for tool in self.config["tools"]: + for action in tool_actions[tool]: + try: + tpls = self.sub_steps[tool].get_output_files(action).values() + except AttributeError: + tpls = self.sub_steps[tool].get_output_files(action) + for tpl in tpls: + filenames = expand( + tpl, + mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], + library_name=[sample_pair.tumor_sample.dna_ngs_library.name], + ) + for f in filenames: + if ".tmp." not in f: + yield f.replace("work/", "output/") + + def check_config(self): + """Check that the necessary globalc onfiguration is present""" + self.ensure_w_config( + ("static_data_config", "reference", "path"), + "Path to reference FASTA file not configured but required", + ) diff --git a/snappy_wrappers/wrappers/scarHRD/environment.yaml b/snappy_wrappers/wrappers/scarHRD/environment.yaml new file mode 100644 index 000000000..b6a8c8b49 --- /dev/null +++ b/snappy_wrappers/wrappers/scarHRD/environment.yaml @@ -0,0 +1,10 @@ +channels: + - conda-forge + - bioconda +dependencies: + - python =3.9 + - sequenza-utils + - r-sequenza + - r-devtools + - r-data.table + - samtools diff --git a/snappy_wrappers/wrappers/scarHRD/gcreference/environment.yaml b/snappy_wrappers/wrappers/scarHRD/gcreference/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/scarHRD/gcreference/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/scarHRD/gcreference/wrapper.py b/snappy_wrappers/wrappers/scarHRD/gcreference/wrapper.py new file mode 100644 index 000000000..1b9a2c4b0 --- /dev/null +++ b/snappy_wrappers/wrappers/scarHRD/gcreference/wrapper.py @@ -0,0 +1,49 @@ +"""CUBI+Snakemake wrapper code for scarHRD (sequenza GC reference file) +""" + +import os + +from snakemake import shell + +__author__ = "Eric Blanc " + +step = snakemake.config["pipeline_step"]["name"] +genome = snakemake.config["static_data_config"]["reference"]["path"] +length = snakemake.config["step_config"][step]["scarHRD"]["length"] + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Also pipe stderr to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +sequenza-utils gc_wiggle --fasta {genome} -w {length} -o {snakemake.output} + +pushd $(dirname {snakemake.output}) +md5sum $(basename {snakemake.output}) > $(basename {snakemake.output}).md5 +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/scarHRD/install/environment.yaml b/snappy_wrappers/wrappers/scarHRD/install/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/scarHRD/install/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/scarHRD/install/wrapper.py b/snappy_wrappers/wrappers/scarHRD/install/wrapper.py new file mode 100644 index 000000000..a9a9c15e0 --- /dev/null +++ b/snappy_wrappers/wrappers/scarHRD/install/wrapper.py @@ -0,0 +1,48 @@ +"""CUBI+Snakemake wrapper code for scarHRD (non-conda package installation) +""" + +import os + +from snakemake import shell + +__author__ = "Eric Blanc " + +lib_path = os.path.dirname(snakemake.output.lib_path) + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Also pipe stderr to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +R --vanilla --slave << __EOF +devtools::install_github("aroneklund/copynumber", lib="{lib_path}", upgrade="never") +devtools::install_github("sztup/scarHRD", lib="{lib_path}", upgrade="never") +__EOF +touch {snakemake.output} +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/scarHRD/run/environment.yaml b/snappy_wrappers/wrappers/scarHRD/run/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/scarHRD/run/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/scarHRD/run/wrapper.py b/snappy_wrappers/wrappers/scarHRD/run/wrapper.py new file mode 100644 index 000000000..6e414eade --- /dev/null +++ b/snappy_wrappers/wrappers/scarHRD/run/wrapper.py @@ -0,0 +1,81 @@ +"""CUBI+Snakemake wrapper code for scarHRD (non-conda package installation) +""" + +import os + +from snakemake import shell + +__author__ = "Eric Blanc " + +lib_path = os.path.dirname(snakemake.input.lib_path) + +step = snakemake.config["pipeline_step"]["name"] +genome = snakemake.config["static_data_config"]["reference"]["path"] +length = snakemake.config["step_config"][step]["scarHRD"]["length"] +genome_name = snakemake.config["step_config"][step]["scarHRD"]["genome_name"] + +chr_in_name = "TRUE" if snakemake.config["step_config"][step]["scarHRD"]["chr_prefix"] else "FALSE" +prefix = "chr" if snakemake.config["step_config"][step]["scarHRD"]["chr_prefix"] else "" +if genome_name == "grch37" or genome_name == "grch38": + chromosomes = " ".join([prefix + str(x) for x in list(range(1, 23)) + ["X", "Y"]]) +elif genome_name == "mouse": + chromosomes = " ".join([prefix + str(x) for x in list(range(1, 21)) + ["X", "Y"]]) +else: + raise Exception("Invalid configuration") + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Also pipe stderr to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +sequenza-utils bam2seqz \ + -gc {snakemake.input.gc} --fasta {genome} \ + -n {snakemake.input.normal_bam} --tumor {snakemake.input.tumor_bam} \ + -C {chromosomes} \ + | sequenza-utils seqz_binning -w {length} -s - \ + | gzip > {snakemake.output.sequenza} + +cat << __EOF | R --vanilla --slave +.libPaths(c("{lib_path}", .libPaths())) +Sys.setenv(VROOM_CONNECTION_SIZE=2000000000) +library("scarHRD") + +tbl <- scar_score("{snakemake.output.sequenza}", reference="{genome_name}", seqz=TRUE, chr.in.name={chr_in_name}) +cat('{{\n', file="{snakemake.output.scarHRD}") +cat(' "HRD": ', tbl[1,1], ',\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) +cat(' "Telomeric AI": ', tbl[1,2], ',\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) +cat(' "LST": ', tbl[1,3], ',\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) +cat(' "HRD-sum": ', tbl[1,4], '\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) +cat('}}\n', file="{snakemake.output.scarHRD}", append=TRUE) + +__EOF + +pushd $(dirname {snakemake.output.sequenza}) ; f=$(basename {snakemake.output.sequenza}) ; md5sum $f > $f.md5 ; popd +pushd $(dirname {snakemake.output.scarHRD}) ; f=$(basename {snakemake.output.scarHRD}) ; md5sum $f > $f.md5 ; popd +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/tests/snappy_pipeline/workflows/test_workflows_homologous_recombination_deficiency.py b/tests/snappy_pipeline/workflows/test_workflows_homologous_recombination_deficiency.py new file mode 100644 index 000000000..3183a63e7 --- /dev/null +++ b/tests/snappy_pipeline/workflows/test_workflows_homologous_recombination_deficiency.py @@ -0,0 +1,200 @@ +# -*- coding: utf-8 -*- +"""Tests for the homologous_recombination_deficiency module code""" + +import textwrap + +import pytest +import ruamel.yaml as ruamel_yaml +from snakemake.io import Wildcards + +from snappy_pipeline.workflows.homologous_recombination_deficiency import ( + HomologousRecombinationDeficiencyWorkflow, +) + +from .common import get_expected_log_files_dict +from .conftest import patch_module_fs + +__author__ = "Eric Blanc" + + +@pytest.fixture(scope="module") # otherwise: performance issues +def minimal_config(): + """Return YAML parsing result for configuration""" + yaml = ruamel_yaml.YAML() + return yaml.load( + textwrap.dedent( + r""" + static_data_config: + reference: + path: /path/to/ref.fa + + step_config: + ngs_mapping: + tools: + dna: ['bwa'] + bwa: + path_index: /path/to/bwa/index.fasta + homologous_recombination_deficiency: + tools: ['scarHRD'] + path_ngs_mapping: ../ngs_mapping # REQUIRED + + data_sets: + first_batch: + file: sheet.tsv + search_patterns: + - {'left': '*/*/*_R1.fastq.gz', 'right': '*/*/*_R2.fastq.gz'} + search_paths: ['/path'] + type: matched_cancer + naming_scheme: only_secondary_id + """ + ).lstrip() + ) + + +@pytest.fixture +def homologous_recombination_deficiency_workflow( + dummy_workflow, + minimal_config, + config_lookup_paths, + work_dir, + config_paths, + cancer_sheet_fake_fs, + mocker, +): + """Return HomologousRecombinationDeficiencyWorkflow object pre-configured with cancer sheet""" + # Patch out file-system related things in abstract (the crawling link in step is defined there) + patch_module_fs("snappy_pipeline.workflows.abstract", cancer_sheet_fake_fs, mocker) + dummy_workflow.globals = {"ngs_mapping": lambda x: "NGS_MAPPING/" + x} + # Construct the workflow object + return HomologousRecombinationDeficiencyWorkflow( + dummy_workflow, + minimal_config, + config_lookup_paths, + config_paths, + work_dir, + ) + + +# Tests for ScarHRDStepPart ------------------------------------------------------------------ + + +def test_scarHRD_step_part_get_input_files_run(homologous_recombination_deficiency_workflow): + """Tests ScarHRDStepPart.get_input_files() - run""" + wildcards = Wildcards(fromdict={"library_name": "P001-T1-DNA1-WGS1", "mapper": "bwa"}) + expected = { + "lib_path": "work/R_packages/out/.done", + "gc": "work/static_data/out/grch37_50.wig.gz", + "normal_bai": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam.bai", + "normal_bam": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam", + "tumor_bai": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam.bai", + "tumor_bam": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam", + } + actual = homologous_recombination_deficiency_workflow.get_input_files("scarHRD", "run")( + wildcards + ) + assert actual == expected + + +def test_scarHRD_step_part_get_output_files_run(homologous_recombination_deficiency_workflow): + """Tests ScarHRDStepPart.get_output_files() - run""" + # Define expected + base_name_out = "work/{mapper}.scarHRD.{library_name}/out/{mapper}.scarHRD.{library_name}" + expected = { + "sequenza": base_name_out + ".seqz.gz", + "scarHRD": base_name_out + ".json", + } + # Get actual + actual = homologous_recombination_deficiency_workflow.get_output_files("scarHRD", "run") + assert actual == expected + + +def test_scarHRD_step_part_get_log_file_run(homologous_recombination_deficiency_workflow): + """Tests ScarHRDStepPart.get_log_file() - run""" + base_name = "work/{mapper}.scarHRD.{library_name}/log/{mapper}.scarHRD.{library_name}" + expected = get_expected_log_files_dict(base_out=base_name) + actual = homologous_recombination_deficiency_workflow.get_log_file("scarHRD", "run") + assert actual == expected + + +def test_scarHRD_step_part_get_resource_usage_run(homologous_recombination_deficiency_workflow): + """Tests ScarHRDStepPart.get_resource() - run""" + # Define expected + expected_dict = {"threads": 2, "time": "48:00:00", "memory": "32G", "partition": "medium"} + # Evaluate + for resource, expected in expected_dict.items(): + msg_error = f"Assertion error for resource '{resource}'." + actual = homologous_recombination_deficiency_workflow.get_resource( + "scarHRD", "run", resource + ) + assert actual == expected, msg_error + + +def test_scarHRD_step_part_get_output_files_install(homologous_recombination_deficiency_workflow): + """Tests ScarHRDStepPart.get_output_files() - install""" + # Define expected + expected = {"lib_path": "work/R_packages/out/.done"} + # Get actual + actual = homologous_recombination_deficiency_workflow.get_output_files("scarHRD", "install") + assert actual == expected + + +def test_scarHRD_step_part_get_log_file_install(homologous_recombination_deficiency_workflow): + """Tests ScarHRDStepPart.get_log_file() - install""" + base_name = "work/R_packages/log/R_packages" + expected = get_expected_log_files_dict(base_out=base_name) + actual = homologous_recombination_deficiency_workflow.get_log_file("scarHRD", "install") + assert actual == expected + + +def test_scarHRD_step_part_get_resource_usage_install(homologous_recombination_deficiency_workflow): + """Tests ScarHRDStepPart.get_resource() - install""" + # Define expected + expected_dict = {"threads": 1, "time": "02:00:00", "memory": "4096M", "partition": "short"} + # Evaluate + for resource, expected in expected_dict.items(): + msg_error = f"Assertion error for resource '{resource}'." + actual = homologous_recombination_deficiency_workflow.get_resource( + "scarHRD", "install", resource + ) + assert actual == expected, msg_error + + +def test_scarHRD_step_part_get_output_files_gcreference( + homologous_recombination_deficiency_workflow, +): + """Tests ScarHRDStepPart.get_output_files() - gcreference""" + # Define expected + expected = {"gc": "work/static_data/out/grch37_50.wig.gz"} + # Get actual + actual = homologous_recombination_deficiency_workflow.get_output_files("scarHRD", "gcreference") + assert actual == expected + + +def test_scarHRD_step_part_get_log_file_gcreference(homologous_recombination_deficiency_workflow): + """Tests ScarHRDStepPart.get_log_file() - gcreference""" + base_name = "work/static_data/log/grch37_50" + expected = get_expected_log_files_dict(base_out=base_name) + actual = homologous_recombination_deficiency_workflow.get_log_file("scarHRD", "gcreference") + assert actual == expected + + +# Tests for SomaticMsiCallingWorkflow -------------------------------------------------------------- + + +def test_homologous_recombination_deficiency_workflow(homologous_recombination_deficiency_workflow): + """Test simple functionality of the workflow""" + # Check created sub steps + expected = ["link_out", "scarHRD"] + assert list(sorted(homologous_recombination_deficiency_workflow.sub_steps.keys())) == expected + # Check result file construction + expected = [ + "output/bwa.scarHRD.P001-T1-DNA1-WGS1/out/bwa.scarHRD.P001-T1-DNA1-WGS1.json", + "output/bwa.scarHRD.P001-T1-DNA1-WGS1/out/bwa.scarHRD.P001-T1-DNA1-WGS1.seqz.gz", + "output/bwa.scarHRD.P002-T1-DNA1-WGS1/out/bwa.scarHRD.P002-T1-DNA1-WGS1.json", + "output/bwa.scarHRD.P002-T1-DNA1-WGS1/out/bwa.scarHRD.P002-T1-DNA1-WGS1.seqz.gz", + "output/bwa.scarHRD.P002-T2-DNA1-WGS1/out/bwa.scarHRD.P002-T2-DNA1-WGS1.json", + "output/bwa.scarHRD.P002-T2-DNA1-WGS1/out/bwa.scarHRD.P002-T2-DNA1-WGS1.seqz.gz", + ] + actual = set(homologous_recombination_deficiency_workflow.get_result_files()) + expected = set(expected) + assert actual == expected From 35b24cd70e4352244b6d09d414c6fae761c7dece Mon Sep 17 00:00:00 2001 From: ericblanc20 Date: Thu, 24 Aug 2023 10:47:18 +0200 Subject: [PATCH 10/19] feat: (430) picard metrics for bam files (#431) --- .../workflows/ngs_data_qc/Snakefile | 39 +++ .../workflows/ngs_data_qc/__init__.py | 231 +++++++++++++++++- .../wrappers/picard/environment.yaml | 6 + .../wrappers/picard/metrics/environment.yaml | 1 + .../wrappers/picard/metrics/wrapper.py | 166 +++++++++++++ .../wrappers/picard/prepare/environment.yaml | 1 + .../wrappers/picard/prepare/wrapper.py | 100 ++++++++ .../workflows/test_workflows_ngs_data_qc.py | 123 +++++++--- ...t_workflows_ngs_data_qc_processed_fastq.py | 2 +- 9 files changed, 624 insertions(+), 45 deletions(-) create mode 100644 snappy_wrappers/wrappers/picard/environment.yaml create mode 120000 snappy_wrappers/wrappers/picard/metrics/environment.yaml create mode 100644 snappy_wrappers/wrappers/picard/metrics/wrapper.py create mode 120000 snappy_wrappers/wrappers/picard/prepare/environment.yaml create mode 100644 snappy_wrappers/wrappers/picard/prepare/wrapper.py diff --git a/snappy_pipeline/workflows/ngs_data_qc/Snakefile b/snappy_pipeline/workflows/ngs_data_qc/Snakefile index 0d379e48c..53ebb9335 100644 --- a/snappy_pipeline/workflows/ngs_data_qc/Snakefile +++ b/snappy_pipeline/workflows/ngs_data_qc/Snakefile @@ -85,3 +85,42 @@ rule data_qc_fastqc_run: wf.get_log_file("fastqc", "run"), wrapper: wf.wrapper_path("fastqc") + + +# Bam Data QC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +# Run picard ------------------------------------------------------------------ + + +rule data_qc_picard_prepare: + output: + **wf.get_output_files("picard", "prepare"), + threads: wf.get_resource("picard", "prepare", "threads") + resources: + time=wf.get_resource("picard", "prepare", "time"), + memory=wf.get_resource("picard", "prepare", "memory"), + partition=wf.get_resource("picard", "prepare", "partition"), + tmpdir=wf.get_resource("picard", "prepare", "tmpdir"), + log: + **wf.get_log_file("picard", "prepare"), + wrapper: + wf.wrapper_path("picard/prepare") + + +rule data_qc_picard_metrics: + input: + unpack(wf.get_input_files("picard", "metrics")), + output: + **wf.get_output_files("picard", "metrics"), + params: + wf.get_params("picard", "metrics"), + threads: wf.get_resource("picard", "metrics", "threads") + resources: + time=wf.get_resource("picard", "metrics", "time"), + memory=wf.get_resource("picard", "metrics", "memory"), + partition=wf.get_resource("picard", "metrics", "partition"), + tmpdir=wf.get_resource("picard", "metrics", "tmpdir"), + log: + **wf.get_log_file("picard", "metrics"), + wrapper: + wf.wrapper_path("picard/metrics") diff --git a/snappy_pipeline/workflows/ngs_data_qc/__init__.py b/snappy_pipeline/workflows/ngs_data_qc/__init__.py index 3268ca84d..3f4d4af76 100644 --- a/snappy_pipeline/workflows/ngs_data_qc/__init__.py +++ b/snappy_pipeline/workflows/ngs_data_qc/__init__.py @@ -17,6 +17,7 @@ from biomedsheets.shortcuts import GenericSampleSheet from snakemake.io import Namedlist, expand, touch +from snappy_pipeline.base import UnsupportedActionException from snappy_pipeline.utils import dictify, listify from snappy_pipeline.workflows.abstract import ( BaseStep, @@ -24,6 +25,7 @@ LinkInPathGenerator, LinkInStep, LinkOutStepPart, + ResourceUsage, get_ngs_library_folder_name, ) @@ -33,9 +35,66 @@ step_config: ngs_data_qc: path_link_in: "" # OPTIONAL Override data set configuration search paths for FASTQ files - tools: [fastqc] # REQUIRED - available: 'fastqc' + tools: [fastqc, picard] # REQUIRED - available: 'fastqc' & 'picard' (for QC on bam files) + picard: + path_ngs_mapping: ../ngs_mapping # REQUIRED + path_to_baits: "" # Required when CollectHsMetrics is among the programs + path_to_targets: "" # When missing, same as baits + bait_name: "" # Exon enrichment kit name (optional) + programs: [] # Available metrics: + # * Generic metrics [* grouped into CollectMultipleMetrics] + # - CollectAlignmentSummaryMetrics * + # - CollectBaseDistributionByCycle * + # - CollectGcBiasMetrics * + # - CollectInsertSizeMetrics * + # - CollectJumpingLibraryMetrics + # - CollectOxoGMetrics + # - CollectQualityYieldMetrics * + # - CollectSequencingArtifactMetrics * + # - EstimateLibraryComplexity + # - MeanQualityByCycle * + # - QualityScoreDistribution * + # * WGS-specific metrics + # - CollectRawWgsMetrics + # - CollectWgsMetrics + # - CollectWgsMetricsWithNonZeroCoverage + # * Other assay-specific metrics + # - CollectHsMetrics Whole Exome Sequencing + # - CollectTargetedPcrMetrics Panel sequencing + # - CollectRnaSeqMetrics mRNA sequencing, not implemented yet + # - CollectRbsMetrics bi-sulfite sequencing, not implemented yet """ +MULTIPLE_METRICS = { + "CollectAlignmentSummaryMetrics": ["alignment_summary_metrics"], + "CollectBaseDistributionByCycle": ["base_distribution_by_cycle_metrics"], + "CollectGcBiasMetrics": ["gc_bias.summary_metrics", "gc_bias.detail_metrics"], + "CollectInsertSizeMetrics": ["insert_size_metrics"], + "CollectQualityYieldMetrics": ["quality_yield_metrics"], + "CollectSequencingArtifactMetrics": [ + "pre_adapter_detail_metrics", + "pre_adapter_summary_metrics", + "bait_bias_summary_metrics", + "bait_bias_detail_metrics", + ], + "MeanQualityByCycle": ["quality_by_cycle_metrics"], + "QualityScoreDistribution": ["quality_distribution_metrics"], +} +ADDITIONAL_METRICS = ( + "CollectJumpingLibraryMetrics", + "CollectOxoGMetrics", + "EstimateLibraryComplexity", +) +WGS_METRICS = ( + "CollectRawWgsMetrics", + "CollectWgsMetrics", + "CollectWgsMetricsWithNonZeroCoverage", +) +WES_METRICS = ("CollectHsMetrics",) +PANEL_METRICS = ("CollectTargetedPcrMetrics",) +RNA_METRICS = ("CollectRnaSeqMetrics",) +BISULFITE_METRICS = ("CollectRbsMetrics",) + class FastQcReportStepPart(BaseStepPart): """(Raw) data QC using FastQC""" @@ -109,6 +168,107 @@ def _collect_reads(self, wildcards, library_name, prefix): yield os.path.join(self.base_path_in, path_infix, filename).format(**wildcards) +class PicardStepPart(BaseStepPart): + """Collect Picard metrics""" + + name = "picard" + actions = ("prepare", "metrics") + + def __init__(self, parent): + super().__init__(parent) + + def get_input_files(self, action): + self._validate_action(action) + if action == "prepare": + raise UnsupportedActionException( + 'Action "prepare" input files must be defined in config' + ) + + return self._get_input_files_metrics + + @dictify + def _get_input_files_metrics(self, wildcards): + if "CollectHsMetrics" in self.config["picard"]["programs"]: + yield "baits", "work/static_data/picard/out/baits.interval_list" + yield "targets", "work/static_data/picard/out/targets.interval_list" + ngs_mapping = self.parent.sub_workflows["ngs_mapping"] + infix = f"{wildcards.mapper}.{wildcards.library_name}" + yield "bam", ngs_mapping(f"output/{infix}/out/{infix}.bam") + + @dictify + def get_output_files(self, action): + if action == "prepare": + yield "baits", "work/static_data/picard/out/baits.interval_list" + yield "targets", "work/static_data/picard/out/targets.interval_list" + elif action == "metrics": + base_out = "work/{mapper}.{library_name}/report/picard/{mapper}.{library_name}." + for pgm in self.config["picard"]["programs"]: + if pgm in MULTIPLE_METRICS.keys(): + first = MULTIPLE_METRICS[pgm][0] + yield pgm, base_out + f"CollectMultipleMetrics.{first}.txt" + yield pgm + "_md5", base_out + f"CollectMultipleMetrics.{first}.txt.md5" + else: + yield pgm, base_out + pgm + ".txt" + yield pgm + "_md5", base_out + pgm + ".txt.md5" + else: + actions_str = ", ".join(self.actions) + raise UnsupportedActionException( + f"Action '{action}' is not supported. Valid options: {actions_str}" + ) + + @dictify + def get_log_file(self, action): + if action == "prepare": + prefix = "work/static_data/picard/log/prepare" + elif action == "metrics": + prefix = "work/{mapper}.{library_name}/log/picard/{mapper}.{library_name}" + else: + actions_str = ", ".join(self.actions) + raise UnsupportedActionException( + f"Action '{action}' is not supported. Valid options: {actions_str}" + ) + + key_ext = ( + ("wrapper", ".wrapper.py"), + ("log", ".log"), + ("conda_info", ".conda_info.txt"), + ("conda_list", ".conda_list.txt"), + ("env_yaml", ".environment.yaml"), + ) + for key, ext in key_ext: + yield key, prefix + ext + yield key + "_md5", prefix + ext + ".md5" + + def get_params(self, action): + self._validate_action(action) + + return self._get_params + + @dictify + def _get_params(self, wildcards): + return {"prefix": f"{wildcards.mapper}.{wildcards.library_name}"} + + def get_resource_usage(self, action): + """Get Resource Usage + + :param action: Action (i.e., step) in the workflow, example: 'run'. + :type action: str + + :return: Returns ResourceUsage for step. + + :raises UnsupportedActionException: if action not in class defined list of valid actions. + """ + if action == "prepare": + return super().get_resource_usage(action) + elif action == "metrics": + return ResourceUsage(threads=1, time="24:00:00", memory="24G") + else: + actions_str = ", ".join(self.actions) + raise UnsupportedActionException( + f"Action '{action}' is not supported. Valid options: {actions_str}" + ) + + class NgsDataQcWorkflow(BaseStep): """Perform NGS raw data QC""" @@ -124,7 +284,11 @@ def default_config_yaml(cls): def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir): super().__init__(workflow, config, config_lookup_paths, config_paths, workdir) - self.register_sub_step_classes((LinkInStep, LinkOutStepPart, FastQcReportStepPart)) + self.register_sub_step_classes( + (LinkInStep, LinkOutStepPart, FastQcReportStepPart, PicardStepPart) + ) + if "picard" in self.config["tools"]: + self.register_sub_workflow("ngs_mapping", self.config["picard"]["path_ngs_mapping"]) @listify def get_result_files(self): @@ -133,17 +297,58 @@ def get_result_files(self): We will process all NGS libraries of all test samples in all sample sheets. """ - from os.path import join - - name_pattern = "{ngs_library.name}" - # TODO: actually link out report files - yield from self._yield_result_files( - join("output", name_pattern, "report", "fastqc", ".done") - ) - - def _yield_result_files(self, tpl, **kwargs): + if "fastqc" in self.config["tools"]: + yield from self._yield_result_files( + tpl="output/{ngs_library.name}/report/fastqc/.done", + allowed_extraction_types=( + "DNA", + "RNA", + ), + ) + if "picard" in self.config["tools"]: + tpl = ( + "output/{mapper}.{ngs_library.name}/report/picard/{mapper}.{ngs_library.name}.{ext}" + ) + exts = [] + for pgm in self.config["picard"]["programs"]: + if pgm in MULTIPLE_METRICS.keys(): + first = MULTIPLE_METRICS[pgm][0] + exts.append(f"CollectMultipleMetrics.{first}.txt") + exts.append(f"CollectMultipleMetrics.{first}.txt.md5") + else: + exts.append(pgm + ".txt") + exts.append(pgm + ".txt.md5") + yield from self._yield_result_files( + tpl=tpl, + allowed_extraction_types=("DNA",), + mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], + ext=exts, + ) + + def _yield_result_files(self, tpl, allowed_extraction_types, **kwargs): """Build output paths from path template and extension list""" for sheet in self.shortcut_sheets: for ngs_library in sheet.all_ngs_libraries: - # extraction_type = ngs_library.test_sample.extra_infos['extractionType'] - yield from expand(tpl, ngs_library=[ngs_library], **kwargs) + extraction_type = ngs_library.test_sample.extra_infos["extractionType"] + if extraction_type in allowed_extraction_types: + yield from expand(tpl, ngs_library=[ngs_library], **kwargs) + + def check_config(self): + if "picard" in self.config["tools"]: + self.ensure_w_config( + ("step_config", "ngs_data_qc", "picard", "path_ngs_mapping"), + "Path to ngs_mapping not configured but required for picard", + ) + programs = self.config["picard"]["programs"] + assert len(programs) > 0, "No selected programs for collecting metrics" + assert all( + pgm in MULTIPLE_METRICS.keys() + or pgm in ADDITIONAL_METRICS + or pgm in WES_METRICS + or pgm in WGS_METRICS + for pgm in programs + ), "Some requested metrics programs are not implemented" + if "CollectHsMetrics" in programs: + assert self.config["picard"][ + "path_to_baits" + ], "Path to baits must be specified when using CollectHsMetrics" diff --git a/snappy_wrappers/wrappers/picard/environment.yaml b/snappy_wrappers/wrappers/picard/environment.yaml new file mode 100644 index 000000000..758c031e7 --- /dev/null +++ b/snappy_wrappers/wrappers/picard/environment.yaml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda +dependencies: + - picard + - bedtools diff --git a/snappy_wrappers/wrappers/picard/metrics/environment.yaml b/snappy_wrappers/wrappers/picard/metrics/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/picard/metrics/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/picard/metrics/wrapper.py b/snappy_wrappers/wrappers/picard/metrics/wrapper.py new file mode 100644 index 000000000..7156197be --- /dev/null +++ b/snappy_wrappers/wrappers/picard/metrics/wrapper.py @@ -0,0 +1,166 @@ +# -*- coding: utf-8 -*- +"""CUBI+Snakemake wrapper code for picard metrics collection: Snakemake wrapper.py +""" + +from snakemake import shell + +__author__ = "Eric Blanc " + +reference = snakemake.config["static_data_config"]["reference"]["path"] +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step]["picard"] + +collect_multiple_metrics_programs = { + "CollectAlignmentSummaryMetrics", + "CollectBaseDistributionByCycle", + "CollectGcBiasMetrics", + "CollectInsertSizeMetrics", + "CollectQualityYieldMetrics", + "CollectSequencingArtifactMetrics", + "MeanQualityByCycle", + "QualityScoreDistribution", +} +collect_multiple_metrics = " ".join( + [ + f"-PROGRAM {pgm}" + for pgm in collect_multiple_metrics_programs.intersection(set(config["programs"])) + ] +) + +# TODO: understand why snakemake.params is a list... +prefix = "" +if "prefix" in snakemake.params[0].keys() and snakemake.params[0]["prefix"]: + prefix = snakemake.params[0]["prefix"] + "." + +name = "null" +if "bait_name" in config.keys() and config["bait_name"]: + name = config["bait_name"] + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +d=$(ls $CONDA_PREFIX/share | grep picard) +picard_jar="$CONDA_PREFIX/share/$d/picard.jar" +if [[ ! -r $picard_jar ]] +then + echo "Can't find picard jar" + exit -1 +fi + +# Also pipe everything to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec &> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Setup auto-cleaned tmpdir +export tmpdir=$(mktemp -d) +trap "rm -rf $tmpdir" EXIT + +d=$(dirname {snakemake.output[0]}) + +if [[ -n "{collect_multiple_metrics}" ]] +then + # Setting METRIC_ACCUMULATION_LEVEL causes issues for some programs + java -jar $picard_jar CollectMultipleMetrics \ + -I {snakemake.input.bam} \ + -O $d/{prefix}CollectMultipleMetrics \ + -R {reference} \ + -FILE_EXTENSION .txt \ + -PROGRAM null \ + {collect_multiple_metrics} +fi + +if [[ "{config[programs]}" == *"EstimateLibraryComplexity"* ]] +then + java -jar $picard_jar EstimateLibraryComplexity \ + -I {snakemake.input.bam} \ + -O $d/{prefix}EstimateLibraryComplexity.txt +fi + +if [[ "{config[programs]}" == *"CollectJumpingLibraryMetrics"* ]] +then + java -jar $picard_jar CollectJumpingLibraryMetrics \ + -I {snakemake.input.bam} \ + -O $d/{prefix}CollectJumpingLibraryMetrics.txt +fi + +if [[ "{config[programs]}" == *"CollectOxoGMetrics"* ]] +then + if [[ -r "{snakemake.config[static_data_config][dbsnp][path]}" ]] + then + dbsnp="-DB_SNP {snakemake.config[static_data_config][dbsnp][path]}" + else + dbsnp="" + fi + java -jar $picard_jar CollectOxoGMetrics \ + -I {snakemake.input.bam} \ + -O $d/{prefix}CollectOxoGMetrics.txt \ + -R {reference} \ + $dbsnp +fi + +if [[ "{config[programs]}" == *"CollectHsMetrics"* ]] +then + java -jar $picard_jar CollectHsMetrics \ + -I {snakemake.input.bam} \ + -O $d/{prefix}CollectHsMetrics.txt \ + -R {reference} \ + -BAIT_SET_NAME {name} \ + -BAIT_INTERVALS {snakemake.input.baits} \ + -TARGET_INTERVALS {snakemake.input.targets} +fi + +if [[ "{config[programs]}" == *"CollectRawWgsMetrics"* ]] +then + java -jar $picard_jar CollectRawWgsMetrics \ + -I {snakemake.input.bam} \ + -O $d/{prefix}CollectRawWgsMetrics.txt \ + -R {reference} +fi + +if [[ "{config[programs]}" == *"CollectWgsMetrics"* ]] +then + java -jar $picard_jar CollectWgsMetrics \ + -I {snakemake.input.bam} \ + -O $d/{prefix}CollectWgsMetrics.txt \ + -R {reference} +fi + +if [[ "{config[programs]}" == *"CollectWgsMetricsWithNonZeroCoverage"* ]] +then + java -jar $picard_jar CollectWgsMetricsWithNonZeroCoverage \ + -I {snakemake.input.bam} \ + -O $d/{prefix}CollectWgsMetricsWithNonZeroCoverage.txt \ + -CHART $d/{prefix}CollectWgsMetricsWithNonZeroCoverage.pdf \ + -R {reference} +fi + +pushd $d +for f in $(ls *.txt) ; do + md5sum $f >$f.md5 +done +popd +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/picard/prepare/environment.yaml b/snappy_wrappers/wrappers/picard/prepare/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/picard/prepare/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/picard/prepare/wrapper.py b/snappy_wrappers/wrappers/picard/prepare/wrapper.py new file mode 100644 index 000000000..b6f146410 --- /dev/null +++ b/snappy_wrappers/wrappers/picard/prepare/wrapper.py @@ -0,0 +1,100 @@ +# -*- coding: utf-8 -*- +"""CUBI+Snakemake wrapper code for converting exome baits & targets from bed to interval lists +""" + +import os +import re + +from snakemake import shell + +__author__ = "Eric Blanc " + +reference = snakemake.config["static_data_config"]["reference"]["path"] +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step]["picard"] + +reference = re.sub("\.fa(sta)?(\.b?gz)?$", ".dict", reference) +assert os.path.exists(reference), "Missing dict of reference fasta" + +baits = config["path_to_baits"] +targets = config.get("path_to_targets", "") + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +d=$(ls $CONDA_PREFIX/share | grep picard) +picard_jar="$CONDA_PREFIX/share/$d/picard.jar" +if [[ ! -r $picard_jar ]] +then + echo "Can't find picar jar" + exit -1 +fi + +# Also pipe everything to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec &> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Setup auto-cleaned tmpdir +export tmpdir=$(mktemp -d) +trap "rm -rf $tmpdir" EXIT + +# Can't pipe to BedToIntervalList (https://github.com/broadinstitute/picard/issues/1890) +bed_to_interval_list() {{ + fn=$1 + f=$(basename $fn) + cut -f 1-3 $fn \ + | bedtools sort -i - \ + | bedtools merge -i - \ + > $tmpdir/$f + java -jar $picard_jar BedToIntervalList \ + -I $tmpdir/$f \ + -O /dev/stdout \ + -SD {reference} +}} + +md5() {{ + fn=$1 + d=$(dirname $fn) + f=$(basename $fn) + pushd $d 1> /dev/null 2>&1 + checksum=$(md5sum $f) + popd 1> /dev/null 2>&1 + echo $checksum +}} + +bed_to_interval_list {baits} > {snakemake.output.baits} +md5 {snakemake.output.baits} > {snakemake.output.baits}.md5 + +if [[ -n "{targets}" ]] +then + bed_to_interval_list {targets} > {snakemake.output.targets} + md5 {snakemake.output.targets} > {snakemake.output.targets}.md5 +else + ln -rs {snakemake.output.baits} {snakemake.output.targets} + ln -rs {snakemake.output.baits}.md5 {snakemake.output.targets}.md5 +fi +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_data_qc.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_data_qc.py index 28a343e75..7056f602c 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_ngs_data_qc.py +++ b/tests/snappy_pipeline/workflows/test_workflows_ngs_data_qc.py @@ -9,6 +9,7 @@ from snappy_pipeline.workflows.ngs_data_qc import NgsDataQcWorkflow +from .common import get_expected_log_files_dict from .conftest import patch_module_fs @@ -24,8 +25,20 @@ def minimal_config(): path: /path/to/ref.fa step_config: + ngs_mapping: + tools: + dna: [bwa] ngs_data_qc: - tools: ['fastqc'] + tools: ['picard'] + picard: + path_ngs_mapping: /NGS_MAPPING + path_to_baits: /path/to/baits + path_to_targets: /path/to/targets + programs: + - CollectAlignmentSummaryMetrics + - CollectOxoGMetrics + - CollectHsMetrics + - CollectWgsMetrics data_sets: first_batch: @@ -53,6 +66,7 @@ def ngs_data_qc( mocker, ): """Return NgsDataQcWorkflow object pre-configured with germline sheet""" + dummy_workflow.globals = {"ngs_mapping": lambda x: "/NGS_MAPPING/" + x} # Patch out file-system related things in abstract (the crawling link in step is defined there) patch_module_fs("snappy_pipeline.workflows.abstract", germline_sheet_fake_fs, mocker) # Patch out files for aligner indices @@ -67,61 +81,98 @@ def ngs_data_qc( ) -# Tests for FastQcReportStepPart ------------------------------------------------------------------- +# Tests for PicardStepPart ------------------------------------------------------------------- -def test_fastqc_step_part_get_args(ngs_data_qc): - """Tests FastQcReportStepPart.get_args()""" +def test_picard_step_part_get_output_files(ngs_data_qc): + """Tests PicardStepPart.get_output_files() - prepare""" # Define expected - wildcards = Wildcards(fromdict={"library_name": "P001-N1-DNA1-WGS1"}) expected = { - "num_threads": 1, - "more_reads": [ - "work/input_links/P001-N1-DNA1-WGS1/FCXXXXXX/L001/P001_R1.fastq.gz", - "work/input_links/P001-N1-DNA1-WGS1/FCXXXXXX/L001/P001_R2.fastq.gz", - ], + "baits": "work/static_data/picard/out/baits.interval_list", + "targets": "work/static_data/picard/out/targets.interval_list", } - # Get actual and assert - actual = ngs_data_qc.get_args("fastqc", "run")(wildcards) + # Get actual + actual = ngs_data_qc.get_output_files("picard", "prepare") assert actual == expected -def test_fastqc_step_part_get_input_files(ngs_data_qc): - """Tests FastQcReportStepPart.get_input_files()""" +def test_picard_step_part_get_log_file(ngs_data_qc): + """Tests PicardStepPart.get_log_file() - prepare""" # Define expected - wildcards = Wildcards(fromdict={"library_name": "P001-N1-DNA1-WGS1"}) - expected = "work/input_links/P001-N1-DNA1-WGS1/.done" + expected = get_expected_log_files_dict( + base_out="work/static_data/picard/log/prepare", + extended=True, + ) + # Get actual + actual = ngs_data_qc.get_log_file("picard", "prepare") + assert actual == expected + + +def test_picard_step_part_get_input_files(ngs_data_qc): + """Tests PicardStepPart.get_input_files() - metrics""" + # Define expected + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-N1-DNA1-WGS1"}) + expected = { + "baits": "work/static_data/picard/out/baits.interval_list", + "targets": "work/static_data/picard/out/targets.interval_list", + "bam": "/NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam", + } # Get actual and assert - actual = ngs_data_qc.get_input_files("fastqc", "run")(wildcards) + actual = ngs_data_qc.get_input_files("picard", "metrics")(wildcards) assert actual == expected -def test_fastqc_step_part_get_output_files(ngs_data_qc): - """Tests FastQcReportStepPart.get_output_files()""" +def test_picard_step_part_get_output_files(ngs_data_qc): + """Tests PicardStepPart.get_output_files() - metrics""" # Define expected - expected = {"fastqc_done": "work/{library_name}/report/fastqc/.done"} + base_out = "work/{mapper}.{library_name}/report/picard/{mapper}.{library_name}." + expected = { + "CollectAlignmentSummaryMetrics": base_out + + "CollectMultipleMetrics.alignment_summary_metrics.txt", + "CollectOxoGMetrics": base_out + "CollectOxoGMetrics.txt", + "CollectHsMetrics": base_out + "CollectHsMetrics.txt", + "CollectWgsMetrics": base_out + "CollectWgsMetrics.txt", + "CollectAlignmentSummaryMetrics_md5": base_out + + "CollectMultipleMetrics.alignment_summary_metrics.txt.md5", + "CollectOxoGMetrics_md5": base_out + "CollectOxoGMetrics.txt.md5", + "CollectHsMetrics_md5": base_out + "CollectHsMetrics.txt.md5", + "CollectWgsMetrics_md5": base_out + "CollectWgsMetrics.txt.md5", + } + # Get actual + actual = ngs_data_qc.get_output_files("picard", "metrics") + assert actual == expected + + +def test_picard_step_part_get_log_file(ngs_data_qc): + """Tests PicardStepPart.get_log_file() - metrics""" + # Define expected + expected = get_expected_log_files_dict( + base_out="work/{mapper}.{library_name}/log/picard/{mapper}.{library_name}", + extended=True, + ) # Get actual - actual = ngs_data_qc.get_output_files("fastqc", "run") + actual = dict(ngs_data_qc.get_log_file("picard", "metrics")) assert actual == expected -def test_fastqc_step_part_get_log_file(ngs_data_qc): - """Tests FastQcReportStepPart.get_log_file()""" +def test_picard_step_part_get_params(ngs_data_qc): + """Tests PicardStepPart.get_params() - metrics""" + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-N1-DNA1-WGS1"}) # Define expected - expected = "work/{library_name}/log/snakemake.fastqc.log" + expected = {"prefix": "bwa.P001-N1-DNA1-WGS1"} # Get actual - actual = ngs_data_qc.get_log_file("fastqc", "run") + actual = ngs_data_qc.get_params("picard", "metrics")(wildcards) assert actual == expected -def test_fastqc_step_part_get_resource_usage(ngs_data_qc): - """Tests FastQcReportStepPart.get_resource_usage()""" +def test_picard_step_part_get_resource_usage(ngs_data_qc): + """Tests PicardStepPart.get_resource_usage() - metrics""" # Define expected: default defined in workflow.abstract - expected_dict = {"threads": 1, "time": "01:00:00", "memory": "2G", "partition": "medium"} + expected_dict = {"threads": 1, "time": "24:00:00", "memory": "24G", "partition": "medium"} # Evaluate for resource, expected in expected_dict.items(): msg_error = f"Assertion error for resource '{resource}'." - actual = ngs_data_qc.get_resource("fastqc", "run", resource) + actual = ngs_data_qc.get_resource("picard", "metrics", resource) assert actual == expected, msg_error @@ -131,7 +182,7 @@ def test_fastqc_step_part_get_resource_usage(ngs_data_qc): def test_ngs_data_qc_workflow_steps(ngs_data_qc): """Tests simple functionality of the workflow: checks if sub steps are created.""" # Check created sub steps - expected = ["fastqc", "link_in", "link_out"] + expected = ["fastqc", "link_in", "link_out", "picard"] actual = list(sorted(ngs_data_qc.sub_steps.keys())) assert actual == expected @@ -140,6 +191,16 @@ def test_ngs_data_qc_workflow_files(ngs_data_qc): """Tests simple functionality of the workflow: checks if file structure is created according to the expected results from the tools.""" # Check result file construction - expected = [f"output/P00{i}-N1-DNA1-WGS1/report/fastqc/.done" for i in range(1, 7)] + expected = [ + f"output/bwa.P00{i}-N1-DNA1-WGS1/report/picard/bwa.P00{i}-N1-DNA1-WGS1.{metric}.txt{ext}" + for i in range(1, 7) + for metric in ( + "CollectHsMetrics", + "CollectMultipleMetrics.alignment_summary_metrics", + "CollectOxoGMetrics", + "CollectWgsMetrics", + ) + for ext in ("", ".md5") + ] actual = sorted(ngs_data_qc.get_result_files()) assert actual == expected diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_data_qc_processed_fastq.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_data_qc_processed_fastq.py index d3f797f4f..096d6b91e 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_ngs_data_qc_processed_fastq.py +++ b/tests/snappy_pipeline/workflows/test_workflows_ngs_data_qc_processed_fastq.py @@ -134,7 +134,7 @@ def test_fastqc_step_part_get_resource_usage(ngs_data_qc): def test_ngs_data_qc_workflow_steps(ngs_data_qc): """Tests simple functionality of the workflow: checks if sub steps are created.""" # Check created sub steps - expected = ["fastqc", "link_in", "link_out"] + expected = ["fastqc", "link_in", "link_out", "picard"] actual = list(sorted(ngs_data_qc.sub_steps.keys())) assert actual == expected From 4fd0c73c4bd75bf4aa5ef9a464713a2c5d4fada1 Mon Sep 17 00:00:00 2001 From: CuongPham <50145360+giacuong171@users.noreply.github.com> Date: Wed, 30 Aug 2023 22:49:21 +0700 Subject: [PATCH 11/19] feat: add missense TMB calculation (#432) Co-authored-by: giacuong171 --- .../somatic_variant_annotation/__init__.py | 4 +- .../tumor_mutational_burden/Snakefile | 2 + .../tumor_mutational_burden/__init__.py | 184 ++++++++++---- .../wrappers/bcftools/TMB/wrapper.py | 62 ++++- .../wrappers/vep/run/environment.yaml | 3 - .../workflows/test_tumor_mutational_burden.py | 239 ++++++++++++++++-- 6 files changed, 405 insertions(+), 89 deletions(-) diff --git a/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py b/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py index 73181a994..cce189e2f 100644 --- a/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py +++ b/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py @@ -75,7 +75,7 @@ EXT_NAMES = ("vcf", "vcf_tbi", "vcf_md5", "vcf_tbi_md5") #: Names of the annotator tools -TOOLS = ("jannovar", "vep") +ANNOTATION_TOOLS = ("jannovar", "vep") #: Default configuration for the somatic_variant_calling step DEFAULT_CONFIG = r""" @@ -336,7 +336,7 @@ def get_result_files(self): annotators = list( map( lambda x: x.replace("jannovar", "jannovar_annotate_somatic_vcf"), - set(self.config["tools"]) & set(TOOLS), + set(self.config["tools"]) & set(ANNOTATION_TOOLS), ) ) callers = set(self.config["tools_somatic_variant_calling"]) diff --git a/snappy_pipeline/workflows/tumor_mutational_burden/Snakefile b/snappy_pipeline/workflows/tumor_mutational_burden/Snakefile index 27da7d775..4ce18d68d 100644 --- a/snappy_pipeline/workflows/tumor_mutational_burden/Snakefile +++ b/snappy_pipeline/workflows/tumor_mutational_burden/Snakefile @@ -59,6 +59,8 @@ rule tumor_mutational_burden_calculation: memory=wf.get_resource("tmb_gathering", "run", "memory"), partition=wf.get_resource("tmb_gathering", "run", "partition"), tmpdir=wf.get_resource("tmb_gathering", "run", "tmpdir"), + params: + **{"args": wf.get_params("tmb_gathering", "run")}, log: **wf.get_log_file("tmb_gathering", "run"), wrapper: diff --git a/snappy_pipeline/workflows/tumor_mutational_burden/__init__.py b/snappy_pipeline/workflows/tumor_mutational_burden/__init__.py index c7176d8fa..0880ba37f 100644 --- a/snappy_pipeline/workflows/tumor_mutational_burden/__init__.py +++ b/snappy_pipeline/workflows/tumor_mutational_burden/__init__.py @@ -5,10 +5,13 @@ from biomedsheets.shortcuts import CancerCaseSheet, CancerCaseSheetOptions, is_not_background from snakemake.io import expand -from snappy_pipeline.base import UnsupportedActionException from snappy_pipeline.utils import dictify, listify from snappy_pipeline.workflows.abstract import BaseStep, BaseStepPart, LinkOutStepPart from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow, ResourceUsage +from snappy_pipeline.workflows.somatic_variant_annotation import ( + ANNOTATION_TOOLS, + SomaticVariantAnnotationWorkflow, +) from snappy_pipeline.workflows.somatic_variant_calling import ( SOMATIC_VARIANT_CALLERS_MATCHED, SomaticVariantCallingWorkflow, @@ -24,10 +27,13 @@ DEFAULT_CONFIG = r""" step_config: tumor_mutational_burden: - path_somatic_variant_calling: ../somatic_variant_calling # REQUIRED + has_annotation: 'TRUE' # REQUIRED + path_somatic_variant: ../somatic_variant_annotation # REQUIRED tools_ngs_mapping: [] # default to those configured for ngs_mapping tools_somatic_variant_calling: [] # default to those configured for somatic_variant_calling + tools_somatic_variant_annotation: [] # default to those configured for somatic_variant_annotation target_regions: # REQUIRED + missense_regex: '.*[\|&]missense_variant[\|&].*' #change if the annotation tool doesn't use 'missense_variant' to indicate missense variant """ @@ -56,23 +62,41 @@ def __init__(self, parent): @dictify def get_input_files(self, action): self._validate_action(action) - tpl = ( - "output/{mapper}.{var_caller}.{tumor_library}/out/" - "{mapper}.{var_caller}.{tumor_library}" - ) + # Adding part for runnng with annotation file instead of with variant calling file + if self.w_config["step_config"]["tumor_mutational_burden"]["has_annotation"] == "TRUE": + tpl = ( + "output/{mapper}.{var_caller}.{anno_tool}.{tumor_library}/out/" + "{mapper}.{var_caller}.{anno_tool}.{tumor_library}" + ) + else: + tpl = ( + "output/{mapper}.{var_caller}.{tumor_library}/out/" + "{mapper}.{var_caller}.{tumor_library}" + ) + key_ext = {"vcf": ".vcf.gz", "vcf_tbi": ".vcf.gz.tbi"} - variant_calling = self.parent.sub_workflows["somatic_variant_calling"] # read + # Adding part for runnng with annotation file instead of with variant calling file + if self.w_config["step_config"]["tumor_mutational_burden"]["has_annotation"] == "TRUE": + variant_path = self.parent.sub_workflows["somatic_variant_annotation"] + else: + variant_path = self.parent.sub_workflows["somatic_variant_calling"] for key, ext in key_ext.items(): - yield key, variant_calling(tpl + ext) + yield key, variant_path(tpl + ext) @dictify def get_output_files(self, action): # Validate action self._validate_action(action) - prefix = ( - "work/{mapper}.{var_caller}.tmb.{tumor_library}/out/" - "{mapper}.{var_caller}.tmb.{tumor_library}" - ) + if self.w_config["step_config"]["tumor_mutational_burden"]["has_annotation"] == "TRUE": + prefix = ( + "work/{mapper}.{var_caller}.{anno_tool}.tmb.{tumor_library}/out/" + "{mapper}.{var_caller}.{anno_tool}.tmb.{tumor_library}" + ) + else: + prefix = ( + "work/{mapper}.{var_caller}.tmb.{tumor_library}/out/" + "{mapper}.{var_caller}.tmb.{tumor_library}" + ) key_ext = {"json": ".json"} for key, ext in key_ext.items(): yield key, prefix + ext @@ -80,11 +104,17 @@ def get_output_files(self, action): @dictify def _get_log_file(self, action): - assert action == "run" - prefix = ( - "work/{mapper}.{var_caller}.tmb.{tumor_library}/log/" - "{mapper}.{var_caller}.tmb.{tumor_library}" - ) + self._validate_action(action) + if self.w_config["step_config"]["tumor_mutational_burden"]["has_annotation"] == "TRUE": + prefix = ( + "work/{mapper}.{var_caller}.{anno_tool}.tmb.{tumor_library}/log/" + "{mapper}.{var_caller}.{anno_tool}.tmb.{tumor_library}" + ) + else: + prefix = ( + "work/{mapper}.{var_caller}.tmb.{tumor_library}/log/" + "{mapper}.{var_caller}.tmb.{tumor_library}" + ) key_ext = ( ("log", ".log"), @@ -95,16 +125,7 @@ def _get_log_file(self, action): yield key, prefix + ext def get_resource_usage(self, action): - """Get Resource Usage - :param action: Action (i.e., step) in the workflow, example: 'run'. - :type action: str - :return: Returns ResourceUsage for step. - :raises UnsupportedActionException: if action not in class defined list of valid actions. - """ - if action not in self.actions: - actions_str = ", ".join(self.actions) - error_message = f"Action '{action}' is not supported. Valid options: {actions_str}" - raise UnsupportedActionException(error_message) + self._validate_action(action) mem_mb = 4 * 1024 # 4GB return ResourceUsage( threads=2, @@ -112,6 +133,15 @@ def get_resource_usage(self, action): memory=f"{mem_mb}M", ) + def get_params(self, action): + self._validate_action(action) + return getattr(self, "_get_params_run") + + def _get_params_run(self, wildcards): + return { + "missense_re": self.w_config["step_config"]["tumor_mutational_burden"]["missense_regex"] + } + class TumorMutationalBurdenCalculationWorkflow(BaseStep): """Perform TMB calculation""" @@ -134,15 +164,27 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) config_lookup_paths, config_paths, workdir, - (SomaticVariantCallingWorkflow, NgsMappingWorkflow), + (SomaticVariantCallingWorkflow, SomaticVariantAnnotationWorkflow, NgsMappingWorkflow), ) # Register sub step classes so the sub steps are available self.register_sub_step_classes((TumorMutationalBurdenCalculationStepPart, LinkOutStepPart)) # Register sub workflows - self.register_sub_workflow( - "somatic_variant_calling", - self.w_config["step_config"]["tumor_mutational_burden"]["path_somatic_variant_calling"], - ) + if self.w_config["step_config"]["tumor_mutational_burden"]["has_annotation"] == "TRUE": + self.register_sub_workflow( + "somatic_variant_annotation", + self.w_config["step_config"]["tumor_mutational_burden"]["path_somatic_variant"], + ) + if not self.w_config["step_config"]["tumor_mutational_burden"][ + "tools_somatic_variant_annotation" + ]: + self.w_config["step_config"]["tumor_mutational_burden"][ + "tools_somatic_variant_annotation" + ] = self.w_config["step_config"]["somatic_variant_annotation"]["tools"] + else: + self.register_sub_workflow( + "somatic_variant_calling", + self.w_config["step_config"]["tumor_mutational_burden"]["path_somatic_variant"], + ) # Copy over "tools" setting from somatic_variant_calling/ngs_mapping if not set here if not self.w_config["step_config"]["tumor_mutational_burden"]["tools_ngs_mapping"]: self.w_config["step_config"]["tumor_mutational_burden"][ @@ -160,26 +202,55 @@ def get_result_files(self): callers = set( self.w_config["step_config"]["tumor_mutational_burden"]["tools_somatic_variant_calling"] ) - name_pattern = "{mapper}.{caller}.tmb.{tumor_library.name}" - yield from self._yield_result_files_matched( - os.path.join("output", name_pattern, "out", name_pattern + "{ext}"), - mapper=self.w_config["step_config"]["tumor_mutational_burden"]["tools_ngs_mapping"], - caller=callers & set(SOMATIC_VARIANT_CALLERS_MATCHED), - ext=EXT_VALUES, - ) - yield from self._yield_result_files_matched( - os.path.join("output", name_pattern, "log", name_pattern + "{ext}"), - mapper=self.w_config["step_config"]["tumor_mutational_burden"]["tools_ngs_mapping"], - caller=callers & set(SOMATIC_VARIANT_CALLERS_MATCHED), - ext=( - ".log", - ".log.md5", - ".conda_info.txt", - ".conda_info.txt.md5", - ".conda_list.txt", - ".conda_list.txt.md5", - ), - ) + if self.w_config["step_config"]["tumor_mutational_burden"]["has_annotation"] == "TRUE": + anno_callers = set( + self.w_config["step_config"]["tumor_mutational_burden"][ + "tools_somatic_variant_annotation" + ] + ) + name_pattern = "{mapper}.{caller}.{anno_caller}.tmb.{tumor_library.name}" + yield from self._yield_result_files_matched( + os.path.join("output", name_pattern, "out", name_pattern + "{ext}"), + mapper=self.w_config["step_config"]["tumor_mutational_burden"]["tools_ngs_mapping"], + caller=callers & set(SOMATIC_VARIANT_CALLERS_MATCHED), + anno_caller=anno_callers & set(ANNOTATION_TOOLS), + ext=EXT_VALUES, + ) + yield from self._yield_result_files_matched( + os.path.join("output", name_pattern, "log", name_pattern + "{ext}"), + mapper=self.w_config["step_config"]["tumor_mutational_burden"]["tools_ngs_mapping"], + caller=callers & set(SOMATIC_VARIANT_CALLERS_MATCHED), + anno_caller=anno_callers & set(ANNOTATION_TOOLS), + ext=( + ".log", + ".log.md5", + ".conda_info.txt", + ".conda_info.txt.md5", + ".conda_list.txt", + ".conda_list.txt.md5", + ), + ) + else: + name_pattern = "{mapper}.{caller}.tmb.{tumor_library.name}" + yield from self._yield_result_files_matched( + os.path.join("output", name_pattern, "out", name_pattern + "{ext}"), + mapper=self.w_config["step_config"]["tumor_mutational_burden"]["tools_ngs_mapping"], + caller=callers & set(SOMATIC_VARIANT_CALLERS_MATCHED), + ext=EXT_VALUES, + ) + yield from self._yield_result_files_matched( + os.path.join("output", name_pattern, "log", name_pattern + "{ext}"), + mapper=self.w_config["step_config"]["tumor_mutational_burden"]["tools_ngs_mapping"], + caller=callers & set(SOMATIC_VARIANT_CALLERS_MATCHED), + ext=( + ".log", + ".log.md5", + ".conda_info.txt", + ".conda_info.txt.md5", + ".conda_list.txt", + ".conda_list.txt.md5", + ), + ) def _yield_result_files_matched(self, tpl, **kwargs): """Build output paths from path template and extension list. @@ -208,8 +279,8 @@ def _yield_result_files_matched(self, tpl, **kwargs): def check_config(self): """Check that the path to the NGS mapping is present""" self.ensure_w_config( - ("step_config", "tumor_mutational_burden", "path_somatic_variant_calling"), - "Path to variant calling not configured but required for tmb calculation", + ("step_config", "tumor_mutational_burden", "path_somatic_variant"), + "Path to variant (directory of vcf files) not configured but required for tmb calculation", ) self.ensure_w_config( @@ -217,3 +288,8 @@ def check_config(self): "Path to target_regions file (bed format)" "not configured but required for tmb calculation", ) + + self.ensure_w_config( + ("step_config", "tumor_mutational_burden", "has_annotation"), + "TMB needs to know wether the vcf is annotated or not", + ) diff --git a/snappy_wrappers/wrappers/bcftools/TMB/wrapper.py b/snappy_wrappers/wrappers/bcftools/TMB/wrapper.py index 6bd7a88ba..f4ab3db0b 100644 --- a/snappy_wrappers/wrappers/bcftools/TMB/wrapper.py +++ b/snappy_wrappers/wrappers/bcftools/TMB/wrapper.py @@ -7,6 +7,12 @@ __author__ = "Pham Gia Cuong" __email__ = "pham.gia-cuong@bih-charite.de" +missense_re = ( + snakemake.params.args["missense_re"] + if "args" in snakemake.params.keys() and "missense_re" in snakemake.params.args.keys() + else "" +) + shell( r""" # ----------------------------------------------------------------------------- @@ -33,23 +39,53 @@ number_indels=$(bcftools view -R $bed_file -v indels --threads 2 -H {snakemake.input.vcf}| wc -l) number_variants=$(bcftools view -R $bed_file --threads 2 -H {snakemake.input.vcf}| wc -l) +if [[ -n "{missense_re}" ]] +then + number_missense_variants=$(bcftools view -R $bed_file --threads 2 -H {snakemake.input.vcf}| grep -E '{missense_re}' | wc -l) +fi + TMB=`echo "1000000*($number_variants/$total_exom_length)" | bc -l ` -cat << EOF > {snakemake.output.json} -{ -"Library_name": {snakemake.wildcards.tumor_library}, -"VCF_file": $name_vcf, -"VCF_md5": $vcf_md5, -"BED_file": $bed_file_name, -"BED_md5": $bed_md5, -"TMB": $TMB, -"Number_variants": $number_variants, -"Number_snvs": $number_snvs, -"Number_indels": $number_indels, -"Total_regions_length": $total_exom_length +missense_TMB=`echo "1000000*($number_missense_variants/$total_exom_length)" | bc -l ` +if [[ {snakemake.config[step_config][tumor_mutational_burden][has_annotation]} == "TRUE" ]] +then + out_file=$(cat << EOF + {{ + "Library_name": {snakemake.wildcards.tumor_library}, + "VCF_file": $name_vcf, + "VCF_md5": $vcf_md5, + "BED_file": $bed_file_name, + "BED_md5": $bed_md5, + "TMB": $TMB, + "missense_TMB": $missense_TMB, + "Number_variants": $number_variants, + "Number_snvs": $number_snvs, + "Number_indels": $number_indels, + "Total_regions_length": $total_exom_length + }} EOF + ) + echo $out_file > {snakemake.output.json} +else + out_file=$(cat << EOF + {{ + "Library_name": {snakemake.wildcards.tumor_library}, + "VCF_file": $name_vcf, + "VCF_md5": $vcf_md5, + "BED_file": $bed_file_name, + "BED_md5": $bed_md5, + "TMB": $TMB, + "Number_variants": $number_variants, + "Number_snvs": $number_snvs, + "Number_indels": $number_indels, + "Total_regions_length": $total_exom_length + }} +EOF + ) + echo $out_file > {snakemake.output.json} +fi + pushd $(dirname {snakemake.output.json}) md5sum $(basename {snakemake.output.json}) > $(basename {snakemake.output.json_md5}) -} """ ) diff --git a/snappy_wrappers/wrappers/vep/run/environment.yaml b/snappy_wrappers/wrappers/vep/run/environment.yaml index 48f171edf..711e58eec 100644 --- a/snappy_wrappers/wrappers/vep/run/environment.yaml +++ b/snappy_wrappers/wrappers/vep/run/environment.yaml @@ -1,8 +1,5 @@ channels: - - conda-forge - bioconda dependencies: - - python - ensembl-vep=102 - - htslib diff --git a/tests/snappy_pipeline/workflows/test_tumor_mutational_burden.py b/tests/snappy_pipeline/workflows/test_tumor_mutational_burden.py index e338ac0a6..e9aa46b22 100644 --- a/tests/snappy_pipeline/workflows/test_tumor_mutational_burden.py +++ b/tests/snappy_pipeline/workflows/test_tumor_mutational_burden.py @@ -14,8 +14,9 @@ from .conftest import patch_module_fs +# Test tumor mutational burden calculation with vcf file from somatic variant calling step @pytest.fixture(scope="module") # otherwise: performance issues -def minimal_config(): +def minimal_config_calling(): """Return YAML parsing result for configuration""" yaml = ruamel_yaml.YAML() return yaml.load( @@ -46,8 +47,9 @@ def minimal_config(): path_target_regions: /path/to/target/regions.bed tumor_mutational_burden: - path_somatic_variant_calling: ../somatic_variant_calling + path_somatic_variant: ../somatic_variant_calling tools_ngs_mapping: [] + has_annotation: 'FALSE' # REQUIRED tools_somatic_variant_calling: [] target_regions: /path/to/regions.bed @@ -65,9 +67,9 @@ def minimal_config(): @pytest.fixture -def tumor_mutational_burden_workflow( +def tumor_mutational_burden_workflow_calling( dummy_workflow, - minimal_config, + minimal_config_calling, config_lookup_paths, work_dir, config_paths, @@ -86,7 +88,7 @@ def tumor_mutational_burden_workflow( # Construct the workflow object return TumorMutationalBurdenCalculationWorkflow( dummy_workflow, - minimal_config, + minimal_config_calling, config_lookup_paths, config_paths, work_dir, @@ -96,7 +98,9 @@ def tumor_mutational_burden_workflow( # Tests for TumorMutationalBurdenCalculationStepPart ----------------------------------------------------- -def test_tumor_mutational_step_part_get_input_files(tumor_mutational_burden_workflow): +def test_tumor_mutational_step_part_get_input_files_calling( + tumor_mutational_burden_workflow_calling, +): """Test TumorMutationalBurdenCalculationStepPart.get_input_files()""" base_out = ( "SOMATIC_VARIANT_CALLING/output/{mapper}.{var_caller}.{tumor_library}/out/" @@ -106,34 +110,36 @@ def test_tumor_mutational_step_part_get_input_files(tumor_mutational_burden_work "vcf": base_out + ".vcf.gz", "vcf_tbi": base_out + ".vcf.gz.tbi", } - actual = tumor_mutational_burden_workflow.get_input_files("tmb_gathering", "run") + actual = tumor_mutational_burden_workflow_calling.get_input_files("tmb_gathering", "run") assert actual == expected -def test_tumor_mutational_step_part_get_output_files(tumor_mutational_burden_workflow): +def test_tumor_mutational_step_part_get_output_files_calling( + tumor_mutational_burden_workflow_calling, +): """Tests TumorMutationalBurdenCalculationStepPart.get_output_files()""" base_out = ( "work/{mapper}.{var_caller}.tmb.{tumor_library}/out/" "{mapper}.{var_caller}.tmb.{tumor_library}" ) expected = get_expected_output_json_files_dict(base_out=base_out) - actual = tumor_mutational_burden_workflow.get_output_files("tmb_gathering", "run") + actual = tumor_mutational_burden_workflow_calling.get_output_files("tmb_gathering", "run") assert actual == expected -def test_tumor_mutational_step_part_get_log_files(tumor_mutational_burden_workflow): +def test_tumor_mutational_step_part_get_log_files_calling(tumor_mutational_burden_workflow_calling): """Tests TumorMutationalBurdenCalculationStepPart.get_log_files()""" base_out = ( "work/{mapper}.{var_caller}.tmb.{tumor_library}/log/" "{mapper}.{var_caller}.tmb.{tumor_library}" ) expected = get_expected_log_files_dict(base_out=base_out) - actual = tumor_mutational_burden_workflow.get_log_file("tmb_gathering", "run") + actual = tumor_mutational_burden_workflow_calling.get_log_file("tmb_gathering", "run") assert actual == expected -def test_tumor_mutational_step_part_get_resource_usage( - tumor_mutational_burden_workflow, +def test_tumor_mutational_step_part_get_resource_usage_calling( + tumor_mutational_burden_workflow_calling, ): """Tests TumorMutationalBurdenCalculationStepPart.get_resource_usage()""" # Define expected @@ -141,18 +147,20 @@ def test_tumor_mutational_step_part_get_resource_usage( # Evaluate for resource, expected in expected_dict.items(): msg_error = f"Assertion error for resource '{resource}'." - actual = tumor_mutational_burden_workflow.get_resource("tmb_gathering", "run", resource) + actual = tumor_mutational_burden_workflow_calling.get_resource( + "tmb_gathering", "run", resource + ) assert actual == expected, msg_error # Tests for TumorMutationalBurdenCalculationWorkflow ------------------------------------------------------- -def test_tumor_mutational_burden_workflow(tumor_mutational_burden_workflow): +def test_tumor_mutational_burden_workflow_calling(tumor_mutational_burden_workflow_calling): """Test simple functionality of the workflow""" # Check created sub steps expected = ["link_out", "tmb_gathering"] - actual = list(sorted(tumor_mutational_burden_workflow.sub_steps.keys())) + actual = list(sorted(tumor_mutational_burden_workflow_calling.sub_steps.keys())) assert actual == expected # Check result file construction @@ -182,5 +190,202 @@ def test_tumor_mutational_burden_workflow(tumor_mutational_burden_workflow): for var_caller in ("mutect2", "scalpel") ] expected = list(sorted(expected)) - actual = list(sorted(tumor_mutational_burden_workflow.get_result_files())) + actual = list(sorted(tumor_mutational_burden_workflow_calling.get_result_files())) + assert expected == actual + + +# Test Tumor mutatinal burden calculation with vcf file from somatic variant annotation step +@pytest.fixture(scope="module") # otherwise: performance issues +def minimal_config_annotation(): + """Return YAML parsing result for configuration""" + yaml = ruamel_yaml.YAML() + return yaml.load( + textwrap.dedent( + r""" + static_data_config: + reference: + path: /path/to/ref.fa + cosmic: + path: /path/to/cosmic.vcf.gz + dbsnp: + path: /path/to/dbsnp.vcf.gz + + step_config: + ngs_mapping: + tools: + dna: ['bwa'] + compute_coverage_bed: true + path_target_regions: /path/to/regions.bed + bwa: + path_index: /path/to/bwa/index.fa + + somatic_variant_calling: + tools: + - mutect2 + - scalpel + scalpel: + path_target_regions: /path/to/target/regions.bed + + somatic_variant_annotation: + tools: ["jannovar", "vep"] + jannovar: + path_jannovar_ser: /path/to/jannover.ser + vep: + path_dir_cache: /path/to/dir/cache + + tumor_mutational_burden: + path_somatic_variant: ../somatic_variant_annotation # REQUIRED + has_annotation: 'TRUE' # REQUIRED + tools_ngs_mapping: [] # default to those configured for ngs_mapping + tools_somatic_variant_calling: [] # default to those configured for somatic_variant_calling + tools_somatic_variant_annotation: [] # default to those configured for somatic_variant_annotation + target_regions: /path/to/regions.bed # REQUIRED + + data_sets: + first_batch: + file: sheet.tsv + search_patterns: + - {'left': '*/*/*_R1.fastq.gz', 'right': '*/*/*_R2.fastq.gz'} + search_paths: ['/path'] + type: matched_cancer + naming_scheme: only_secondary_id + """ + ).lstrip() + ) + + +@pytest.fixture +def tumor_mutational_burden_workflow_annotation( + dummy_workflow, + minimal_config_annotation, + config_lookup_paths, + work_dir, + config_paths, + cancer_sheet_fake_fs, + mocker, +): + """Return TumorMutationalBurdenCalculationWorkflow object pre-configured with cancer sheet""" + # Patch out file-system related things in abstract (the crawling link in step is defined there) + patch_module_fs("snappy_pipeline.workflows.abstract", cancer_sheet_fake_fs, mocker) + # Update the "globals" attribute of the mock workflow (snakemake.workflow.Workflow) so we + # can obtain paths from the function as if we really had a NGSMappingPipelineStep there + dummy_workflow.globals = { + "ngs_mapping": lambda x: "NGS_MAPPING/" + x, + "somatic_variant_calling": lambda x: "SOMATIC_VARIANT_CALLING/" + x, + "somatic_variant_annotation": lambda x: "SOMATIC_VARIANT_ANNOTATION/" + x, + } + # Construct the workflow object + return TumorMutationalBurdenCalculationWorkflow( + dummy_workflow, + minimal_config_annotation, + config_lookup_paths, + config_paths, + work_dir, + ) + + +# Tests for TumorMutationalBurdenCalculationStepPart ----------------------------------------------------- + + +def test_tumor_mutational_step_part_get_input_files_annotation( + tumor_mutational_burden_workflow_annotation, +): + """Test TumorMutationalBurdenCalculationStepPart.get_input_files()""" + base_out = ( + "SOMATIC_VARIANT_ANNOTATION/output/{mapper}.{var_caller}.{anno_tool}.{tumor_library}/out/" + "{mapper}.{var_caller}.{anno_tool}.{tumor_library}" + ) + expected = { + "vcf": base_out + ".vcf.gz", + "vcf_tbi": base_out + ".vcf.gz.tbi", + } + actual = tumor_mutational_burden_workflow_annotation.get_input_files("tmb_gathering", "run") + assert actual == expected + + +def test_tumor_mutational_step_part_get_output_files_annotation( + tumor_mutational_burden_workflow_annotation, +): + """Tests TumorMutationalBurdenCalculationStepPart.get_output_files()""" + base_out = ( + "work/{mapper}.{var_caller}.{anno_tool}.tmb.{tumor_library}/out/" + "{mapper}.{var_caller}.{anno_tool}.tmb.{tumor_library}" + ) + expected = get_expected_output_json_files_dict(base_out=base_out) + actual = tumor_mutational_burden_workflow_annotation.get_output_files("tmb_gathering", "run") + assert actual == expected + + +def test_tumor_mutational_step_part_get_log_files_annotation( + tumor_mutational_burden_workflow_annotation, +): + """Tests TumorMutationalBurdenCalculationStepPart.get_log_files()""" + base_out = ( + "work/{mapper}.{var_caller}.{anno_tool}.tmb.{tumor_library}/log/" + "{mapper}.{var_caller}.{anno_tool}.tmb.{tumor_library}" + ) + expected = get_expected_log_files_dict(base_out=base_out) + actual = tumor_mutational_burden_workflow_annotation.get_log_file("tmb_gathering", "run") + assert actual == expected + + +def test_tumor_mutational_step_part_get_resource_usage_annotation( + tumor_mutational_burden_workflow_annotation, +): + """Tests TumorMutationalBurdenCalculationStepPart.get_resource_usage()""" + # Define expected + expected_dict = {"threads": 2, "time": "1:00:00", "memory": "4096M"} + # Evaluate + for resource, expected in expected_dict.items(): + msg_error = f"Assertion error for resource '{resource}'." + actual = tumor_mutational_burden_workflow_annotation.get_resource( + "tmb_gathering", "run", resource + ) + assert actual == expected, msg_error + + +# Tests for TumorMutationalBurdenCalculationWorkflow ------------------------------------------------------- + + +def test_tumor_mutational_burden_workflow_annotation(tumor_mutational_burden_workflow_annotation): + """Test simple functionality of the workflow""" + # Check created sub steps + expected = ["link_out", "tmb_gathering"] + actual = list(sorted(tumor_mutational_burden_workflow_annotation.sub_steps.keys())) + assert actual == expected + + # Check result file construction + tpl = ( + "output/{mapper}.{var_caller}.{anno_tool}.tmb.P00{i}-T{t}-DNA1-WGS1/{dir_}/" + "{mapper}.{var_caller}.{anno_tool}.tmb.P00{i}-T{t}-DNA1-WGS1.{ext}" + ) + expected = [ + tpl.format( + mapper=mapper, var_caller=var_caller, anno_tool=anno_tool, i=i, t=t, ext=ext, dir_="out" + ) + for i, t in ((1, 1), (2, 1), (2, 2)) + for ext in ("json", "json.md5") + for mapper in ("bwa",) + for var_caller in ("mutect2", "scalpel") + for anno_tool in ("jannovar", "vep") + ] + expected += [ + tpl.format( + mapper=mapper, var_caller=var_caller, anno_tool=anno_tool, i=i, t=t, ext=ext, dir_="log" + ) + for i, t in ((1, 1), (2, 1), (2, 2)) + for ext in ( + "conda_info.txt", + "conda_list.txt", + "log", + "conda_info.txt.md5", + "conda_list.txt.md5", + "log.md5", + ) + for mapper in ("bwa",) + for var_caller in ("mutect2", "scalpel") + for anno_tool in ("jannovar", "vep") + ] + expected = list(sorted(expected)) + actual = list(sorted(tumor_mutational_burden_workflow_annotation.get_result_files())) assert expected == actual From ac1a34f44addde7a654a8df991a964c2d41dda37 Mon Sep 17 00:00:00 2001 From: Max Xiaohang Zhao Date: Wed, 13 Sep 2023 15:52:03 +0200 Subject: [PATCH 12/19] docs: add warning for writing new workflow steps (#400) --- docs/dev_intro.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/dev_intro.rst b/docs/dev_intro.rst index 33c5c2fa8..4a7f6a32d 100644 --- a/docs/dev_intro.rst +++ b/docs/dev_intro.rst @@ -99,6 +99,9 @@ Usually, you define a :class:`BaseStep ` instance as the values for the ``input:``, ``output:``, etc. sections of your ``Snakefile``. +.. warning:: + By convention your new Workflow step should be instantiated as ``wf = StepClass(...)`` in the ``Snakefile`` during object setup. Otherwise tools including cubi-tk might not be able to detect and parse your step. See existing workflow ``Snakefile`` for reference. + The :class:`BaseStep ` sub class itself uses :class:`BaseStepPart ` sub classes for the implementation of the individual parts. One part might be linking in FASTQ files from the raw input directory or linking from the ``work/`` to the ``output/`` directory. Another part might be the somatic variant calling using mutect or WGS SV calling using Delly2. From c28d67e23246d319fa88a20331d2324eee379a9f Mon Sep 17 00:00:00 2001 From: ericblanc20 Date: Thu, 14 Sep 2023 12:05:22 +0200 Subject: [PATCH 13/19] feat: 438 vep annotation order (#441) --- .../workflows/cbioportal_export/__init__.py | 9 +- .../somatic_variant_annotation/Snakefile | 2 +- .../somatic_variant_annotation/__init__.py | 63 +++++- .../wrappers/cbioportal/merge_tables/script.R | 7 +- .../jannovar/annotate_somatic_vcf/wrapper.py | 14 +- .../vcf2maf/vcf_to_table/jannovar.yaml | 1 + .../vcf_to_table/protein_mutation_parser.py | 32 ++- .../wrappers/vcf2maf/vcf_to_table/vep.yaml | 1 + .../wrappers/vep/post_filter/wrapper.py | 195 ++++++++++++++++++ snappy_wrappers/wrappers/vep/run/wrapper.py | 30 ++- .../test_workflows_cbioportal_export.py | 10 +- ...st_workflows_somatic_variant_annotation.py | 12 ++ 12 files changed, 345 insertions(+), 31 deletions(-) create mode 100644 snappy_wrappers/wrappers/vep/post_filter/wrapper.py diff --git a/snappy_pipeline/workflows/cbioportal_export/__init__.py b/snappy_pipeline/workflows/cbioportal_export/__init__.py index a864151fa..d5889f5c6 100644 --- a/snappy_pipeline/workflows/cbioportal_export/__init__.py +++ b/snappy_pipeline/workflows/cbioportal_export/__init__.py @@ -5,9 +5,6 @@ snappy_pipeline. It does the necessary data transformations to comply with the formats expected by cBioPortal and writes out the necessary metadata and data files. - -The output is a archive (tarball) that can be uploaded to a cbioportal instance -for import. """ from collections import OrderedDict @@ -436,11 +433,11 @@ def __init__(self, parent): def get_args(self, action): # Validate action self._validate_action(action) - if action == "gistic": - return {"action_type": "gistic", "extra_args": {"pipeline_id": "ENSEMBL"}} if action == "log2": + return {"action_type": "log2", "extra_args": {"pipeline_id": "ENSEMBL"}} + if action == "gistic": return { - "action_type": "log2", + "action_type": "gistic", "extra_args": { "pipeline_id": "ENSEMBL", "amplification": "9", diff --git a/snappy_pipeline/workflows/somatic_variant_annotation/Snakefile b/snappy_pipeline/workflows/somatic_variant_annotation/Snakefile index ebf7d89ed..a0dd7e158 100644 --- a/snappy_pipeline/workflows/somatic_variant_annotation/Snakefile +++ b/snappy_pipeline/workflows/somatic_variant_annotation/Snakefile @@ -92,7 +92,7 @@ rule somatic_variant_annotation_jannovar_annotate_somatic_vcf: log: **wf.get_log_file("jannovar", "annotate_somatic_vcf"), wrapper: - wf.wrapper_path("jannovar_par/annotate_somatic_vcf") + wf.wrapper_path("jannovar/annotate_somatic_vcf") # Variant Statistics Computation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py b/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py index cce189e2f..df2a2d6f7 100644 --- a/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py +++ b/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py @@ -26,7 +26,31 @@ Step Output =========== -TODO +Users can annotate all genes & transcripts overlapping with the variant locus, or +they can select one representative gene and transcript for annotation. +In the latter case, the output vcf file will only contain one annotation per variant, while +in the former case, there might be over 100 annotations for each variant. + +The ordering of features driving the representative annotation choice is under user control. +The default order is: + +1. ``biotype``: protein coding genes come first, it is unclear what is the order for other types of genes +2. ``mane``: the `MANE transcript `_ is selected before other transcripts +3. ``appris``: the `APPRIS principal isoform `_ is selected before alternates +4. ``tsl``: `Transcript Support Level `_ values in increasing order +5. ``ccds``: Transcripts with `CCDS `_ ids are selected before those without +6. ``canonical``: ENSEMBL canonical transcripts are selected before the others +7. ``rank``: VEP internal ranking is used +8. ``length``: longer transcripts are preferred to shorter ones + +This order is (hopefully) suitable for cBioPortal export, as well defined transcripts from protein-coding genes are selected when possible. +However, it is recommended to check the full annotation for variants in or nearby disease-relevant genes. + +All annotators generate a vcf with one annotation per transcript, and some annotators +(only ENSEMBL's Variant Effect Predictor in the current implementation) can also produce another +output containing all annotations. +The single annotation vcf is named ``...vcf.gz`` and +the full annotation output is named ``...full.vcf.gz`` ==================== Global Configuration @@ -115,7 +139,7 @@ assembly: GRCh38 cache_version: 102 # WARNING- this must match the wrapper's vep version! tx_flag: "gencode_basic" # The flag selecting the transcripts. One of "gencode_basic", "refseq", and "merged". - pick: yes # Other option: no (report one or all consequences) + pick_order: ["biotype", "mane", "appris", "tsl", "ccds", "canonical", "rank", "length"] num_threads: 8 buffer_size: 1000 output_options: @@ -131,6 +155,9 @@ class AnnotateSomaticVcfStepPart(BaseStepPart): The ``tumor_library`` wildcard can actually be the name of a donor! """ + #: Only creates vcf with one annotation per variant + has_full = False + def __init__(self, parent): super().__init__(parent) # Build shortcut from cancer bio sample name to matched cancre sample @@ -169,6 +196,9 @@ def get_output_files(self, action): "{{mapper}}.{{var_caller}}.{annotator}.{{tumor_library}}" ).format(annotator=self.annotator) key_ext = {"vcf": ".vcf.gz", "vcf_tbi": ".vcf.gz.tbi"} + if self.has_full: + key_ext["full"] = ".full.vcf.gz" + key_ext["full_tbi"] = ".full.vcf.gz.tbi" for key, ext in key_ext.items(): yield key, prefix + ext yield key + "_md5", prefix + ext + ".md5" @@ -261,6 +291,12 @@ class VepAnnotateSomaticVcfStepPart(AnnotateSomaticVcfStepPart): #: Class available actions actions = ("run",) + #: Also creates vcf with all annotations + has_full = True + + #: Allowed keywords for pick order + PICK_ORDER = ("biotype", "mane", "appris", "tsl", "ccds", "canonical", "rank", "length") + def get_resource_usage(self, action): """Get Resource Usage @@ -282,8 +318,10 @@ def check_config(self): return if not self.config["vep"]["tx_flag"] in ("merged", "refseq", "gencode_basic"): raise InvalidConfiguration("tx_flag must be 'gencode_basic', or 'merged' or 'refseq'") - if not self.config["vep"]["pick"] in ("yes", "no"): - raise InvalidConfiguration("pick must be either 'yes' or 'no'") + if not all([x in self.PICK_ORDER for x in self.config["vep"]["pick_order"]]): + raise InvalidConfiguration( + "pick order keywords must be in {}".format(", ".join(self.PICK_ORDER)) + ) class SomaticVariantAnnotationWorkflow(BaseStep): @@ -362,6 +400,23 @@ def get_result_files(self): ".conda_list.txt.md5", ), ) + # Annotators with full output + full = list( + map( + lambda x: x.replace("jannovar", "jannovar_annotate_somatic_vcf"), + filter( + lambda x: self.sub_steps[x].has_full, + set(self.config["tools"]) & set(ANNOTATION_TOOLS), + ), + ) + ) + yield from self._yield_result_files_matched( + os.path.join("output", name_pattern, "out", name_pattern + ".full{ext}"), + mapper=self.config["tools_ngs_mapping"], + caller=callers & set(SOMATIC_VARIANT_CALLERS_MATCHED), + annotator=full, + ext=EXT_VALUES, + ) # joint calling name_pattern = "{mapper}.{caller}.{annotator}.{donor.name}" yield from self._yield_result_files_joint( diff --git a/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R b/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R index 0b0aada8a..a48a5a848 100644 --- a/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R +++ b/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R @@ -37,13 +37,13 @@ merge_tables <- function(fns, mappings, type=c("log2", "gistic", "segment", "exp } if (type == "gistic") { - stopifnot(all(c("pipeline_id") %in% names(args))) + stopifnot(all(c("pipeline_id", "amplification") %in% names(args))) # Copy numbers (in "cn" column) are transformed into (pseudo-) gistic codes: # 0: Deep deletion, 1: heterozygous deletion, 2: copy number neutral, 3: gain, 4: amplification # In https://doi.org/10.1038/s41586-022-04738-6, the amplification is defined as # copy number greater or equal to 9 copies (args$amplification = 9). args$amplification <- as.numeric(args$amplification) - cn <- read_sample_files(fns, args$pipeline_id, "cn") + cn <- round(read_sample_files(fns, args$pipeline_id, "cn")) cn[args$amplification<=cn] <- args$amplification cn[2 $f.md5 +md5sum $f.tbi > $f.tbi.md5 +popd +""" +) diff --git a/snappy_wrappers/wrappers/vep/run/wrapper.py b/snappy_wrappers/wrappers/vep/run/wrapper.py index 6c46f87de..f4308d9b1 100644 --- a/snappy_wrappers/wrappers/vep/run/wrapper.py +++ b/snappy_wrappers/wrappers/vep/run/wrapper.py @@ -10,8 +10,11 @@ # Get shortcuts to step configuration current_step = snakemake.config["pipeline_step"]["name"] vep_config = snakemake.config["step_config"][current_step]["vep"] +pick_order = ",".join(vep_config["pick_order"]) script_output_options = " ".join(["--" + x for x in vep_config["output_options"]]) +full = snakemake.output.full if "full" in snakemake.output.keys() else "" + shell( r""" set -x @@ -27,6 +30,28 @@ fi fi +if [[ -n "{full}" ]] +then + vep --verbose --force_overwrite --offline --cache \ + --fork {vep_config[num_threads]} --buffer_size {vep_config[buffer_size]} \ + --species {vep_config[species]} --cache_version {vep_config[cache_version]} --assembly {vep_config[assembly]} \ + $(if [[ ! -z "{vep_config[cache_dir]}" ]]; then \ + echo --dir_cache {vep_config[cache_dir]} + fi) \ + {script_output_options} \ + --{vep_config[tx_flag]} \ + --fasta {snakemake.config[static_data_config][reference][path]} \ + --input_file {snakemake.input.vcf} --format vcf \ + --output_file {full} --vcf --compress_output bgzip + tabix {full} + + pushd $(dirname {full}) + f=$(basename {full}) + md5sum $f > $f.md5 + md5sum $f.tbi > $f.tbi.md5 + popd +fi + vep --verbose --force_overwrite --offline --cache \ --fork {vep_config[num_threads]} --buffer_size {vep_config[buffer_size]} \ --species {vep_config[species]} --cache_version {vep_config[cache_version]} --assembly {vep_config[assembly]} \ @@ -34,14 +59,11 @@ echo --dir_cache {vep_config[cache_dir]} fi) \ {script_output_options} \ - $(if [[ "{vep_config[pick]}" = "yes" ]]; then \ - echo "--pick" - fi) \ + --pick --pick_order {pick_order} \ --{vep_config[tx_flag]} \ --fasta {snakemake.config[static_data_config][reference][path]} \ --input_file {snakemake.input.vcf} --format vcf \ --output_file {snakemake.output.vcf} --vcf --compress_output bgzip - tabix {snakemake.output.vcf} pushd $(dirname {snakemake.output.vcf}) diff --git a/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py b/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py index 965c5e758..d225952e9 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py +++ b/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py @@ -528,10 +528,7 @@ def test_cbioportal_cna_step_part_get_args_log2(cbioportal_export_workflow): """Tests cbioportalCnaFilesStepPart.get_args() -action 'log2'""" # Define expected base_name_out = "work/log/cbioportal_cna" - expected = { - "action_type": "log2", - "extra_args": {"amplification": "9", "pipeline_id": "ENSEMBL"}, - } + expected = {"action_type": "log2", "extra_args": {"pipeline_id": "ENSEMBL"}} # Get actual actual = cbioportal_export_workflow.get_args("cbioportal_cna", "log2") assert actual == expected @@ -541,7 +538,10 @@ def test_cbioportal_cna_step_part_get_args_gistic(cbioportal_export_workflow): """Tests cbioportalCnaFilesStepPart.get_args() -action 'gistic'""" # Define expected base_name_out = "work/log/cbioportal_cna" - expected = {"action_type": "gistic", "extra_args": {"pipeline_id": "ENSEMBL"}} + expected = { + "action_type": "gistic", + "extra_args": {"amplification": "9", "pipeline_id": "ENSEMBL"}, + } # Get actual actual = cbioportal_export_workflow.get_args("cbioportal_cna", "gistic") assert actual == expected diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_annotation.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_annotation.py index 2fa469687..d6f0731d8 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_annotation.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_annotation.py @@ -181,6 +181,8 @@ def test_vep_step_part_get_output_files(somatic_variant_annotation_workflow): "{mapper}.{var_caller}.vep.{tumor_library}" ) expected = get_expected_output_vcf_files_dict(base_out=base_out) + full = {k.replace("vcf", "full"): v.replace(".vcf", ".full.vcf") for k, v in expected.items()} + expected = {**expected, **full} actual = somatic_variant_annotation_workflow.get_output_files("vep", "run") assert actual == expected @@ -240,6 +242,16 @@ def test_somatic_variant_annotation_workflow(somatic_variant_annotation_workflow for var_caller in ("mutect", "scalpel") for annotator in ("jannovar_annotate_somatic_vcf", "vep") ] + expected += [ + tpl.format( + mapper=mapper, var_caller=var_caller, annotator=annotator, i=i, t=t, ext=ext, dir_="out" + ) + for i, t in ((1, 1), (2, 1), (2, 2)) + for ext in ("full.vcf.gz", "full.vcf.gz.md5", "full.vcf.gz.tbi", "full.vcf.gz.tbi.md5") + for mapper in ("bwa",) + for var_caller in ("mutect", "scalpel") + for annotator in ("vep",) + ] expected += [ tpl.format( mapper=mapper, var_caller=var_caller, annotator=annotator, i=i, t=t, ext=ext, dir_="log" From 98825db29d3583780b6543b9f5456e0be5e9978b Mon Sep 17 00:00:00 2001 From: Max Xiaohang Zhao Date: Mon, 18 Sep 2023 15:46:00 +0200 Subject: [PATCH 14/19] fix: Fixing feature-effects compression (#440) --- snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py | 1 + 1 file changed, 1 insertion(+) diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py index 55f8d6dbd..671048469 100644 --- a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py +++ b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py @@ -109,6 +109,7 @@ cat $TMPDIR/feature-effects.tsv \ | tr '\n' '\t' \ | sed -e 's/\t$/\n/g' \ +| gzip \ >{snakemake.output.feature_effects} # Perform Mehari structural variant annotation. From 0ca23f645d38130ac08f85b1861ae795f62f96b2 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 18 Sep 2023 15:46:47 +0200 Subject: [PATCH 15/19] feat: bump and fix Mehari for SVs in varfish_export (#444) --- .../wrappers/mehari/annotate_strucvars/wrapper.py | 5 +++++ snappy_wrappers/wrappers/mehari/environment.yaml | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py index 671048469..7b5f9386f 100644 --- a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py +++ b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py @@ -80,6 +80,11 @@ --output-vcf $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf bcftools sort -o $TMPDIR/fixed_bnd_to_inv.$num.vcf $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf + # Fixup SVLEN=1 to SVLEN=. + sed -i -e 's/ID=SVLEN,Number=1/ID=SVLEN,Number=./g' $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf + # Fixup MELT header + sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf + # Add the missing "GT" tag echo '##FORMAT=' \ > $TMPDIR/header.gt.txt diff --git a/snappy_wrappers/wrappers/mehari/environment.yaml b/snappy_wrappers/wrappers/mehari/environment.yaml index 8461e28b2..58ca64f7a 100644 --- a/snappy_wrappers/wrappers/mehari/environment.yaml +++ b/snappy_wrappers/wrappers/mehari/environment.yaml @@ -5,7 +5,7 @@ dependencies: - bcftools >=1.9 - htslib >=1.9 - samtools >=1.9 - - mehari ==0.6.2 + - mehari ==0.7.0 - jq - vcfpy - pysam From 46b2303d4ec185409dc028fa1d1d15b3d2238507 Mon Sep 17 00:00:00 2001 From: ericblanc20 Date: Wed, 20 Sep 2023 08:57:37 +0200 Subject: [PATCH 16/19] fix: fix trimadap-mt & bbduk java version (#446) --- snappy_wrappers/wrappers/bbduk/environment.yaml | 1 + snappy_wrappers/wrappers/bwa/wrapper.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/snappy_wrappers/wrappers/bbduk/environment.yaml b/snappy_wrappers/wrappers/bbduk/environment.yaml index f3f77827a..c7edb6027 100644 --- a/snappy_wrappers/wrappers/bbduk/environment.yaml +++ b/snappy_wrappers/wrappers/bbduk/environment.yaml @@ -3,3 +3,4 @@ channels: - bioconda dependencies: - bbmap =39 + - openjdk >= 8 diff --git a/snappy_wrappers/wrappers/bwa/wrapper.py b/snappy_wrappers/wrappers/bwa/wrapper.py index 7da7a9097..980c6f281 100644 --- a/snappy_wrappers/wrappers/bwa/wrapper.py +++ b/snappy_wrappers/wrappers/bwa/wrapper.py @@ -74,7 +74,7 @@ set -x if [[ "{snakemake.config[step_config][ngs_mapping][bwa][trim_adapters]}" == "True" ]]; then - trimadapt-mt -p {snakemake.config[step_config][ngs_mapping][bwa][num_threads_trimming]} + trimadap-mt -p {snakemake.config[step_config][ngs_mapping][bwa][num_threads_trimming]} else cat # TODO: can we somehow remove this? fi From 55146c7f50fb22f38609b40b3e91cf891bbcaf87 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicolai=20von=20K=C3=BCgelgen?= Date: Wed, 11 Oct 2023 15:18:44 +0200 Subject: [PATCH 17/19] fix: mehari wrapper vcf preprocessing does not actually fix info svlen header (#450) (#451) --- snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py index 7b5f9386f..f2e9b415c 100644 --- a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py +++ b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py @@ -81,9 +81,9 @@ bcftools sort -o $TMPDIR/fixed_bnd_to_inv.$num.vcf $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf # Fixup SVLEN=1 to SVLEN=. - sed -i -e 's/ID=SVLEN,Number=1/ID=SVLEN,Number=./g' $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf + sed -i -e 's/ID=SVLEN,Number=1/ID=SVLEN,Number=./g' $TMPDIR/fixed_bnd_to_inv.$num.vcf # Fixup MELT header - sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf + sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv.$num.vcf # Add the missing "GT" tag echo '##FORMAT=' \ From e394e8cd4bd76eef4725bbaa9ff7711ab5aa9dcc Mon Sep 17 00:00:00 2001 From: ericblanc20 Date: Wed, 11 Oct 2023 16:14:24 +0200 Subject: [PATCH 18/19] feat: PureCN implementation (#453) --- snappy_pipeline/apps/snappy_snake.py | 2 + .../Snakefile | 24 +- .../__init__.py | 148 +++---- .../workflows/panel_of_normals/Snakefile | 66 ++++ .../workflows/panel_of_normals/__init__.py | 313 ++++++++++----- .../Snakefile | 110 ++++++ .../__init__.py | 372 ++++++++++++++---- .../wrappers/mutect2/create_panel/wrapper.py | 32 +- .../coverage}/environment.yaml | 0 .../wrappers/purecn/coverage/wrapper.py | 100 +++++ .../create_panel}/environment.yaml | 0 .../wrappers/purecn/create_panel/wrapper.py | 100 +++++ .../wrappers/purecn/environment.yaml | 5 + .../wrappers/purecn/prepare/environment.yaml | 1 + .../wrappers/purecn/prepare/wrapper.py | 108 +++++ .../wrappers/purecn/run/environment.yaml | 1 + .../wrappers/purecn/run/wrapper.py | 128 ++++++ snappy_wrappers/wrappers/r/environment.yaml | 7 + snappy_wrappers/wrappers/r/wrapper.py | 69 ++++ .../wrappers/scarHRD/environment.yaml | 6 +- .../wrappers/scarHRD/run/wrapper.py | 18 +- .../wrappers/sequenza/environment.yaml | 10 + .../sequenza/gcreference/environment.yaml | 1 + .../gcreference/wrapper.py | 11 +- .../wrappers/sequenza/report/environment.yaml | 1 + .../wrappers/sequenza/report/wrapper.py | 98 +++++ .../wrappers/sequenza/run/environment.yaml | 1 + .../wrappers/sequenza/run/wrapper.py | 71 ++++ .../wrappers/singularity/environment.yaml | 2 + .../install => singularity}/wrapper.py | 37 +- ...ows_homologous_recombination_deficiency.py | 77 ++-- .../test_workflows_panel_of_normals.py | 173 +++++++- .../test_workflows_panel_of_normals_wgs.py | 2 +- ...kflows_somatic_targeted_seq_cnv_calling.py | 246 +++++++++++- 34 files changed, 1941 insertions(+), 399 deletions(-) rename snappy_wrappers/wrappers/{scarHRD/gcreference => purecn/coverage}/environment.yaml (100%) create mode 100644 snappy_wrappers/wrappers/purecn/coverage/wrapper.py rename snappy_wrappers/wrappers/{scarHRD/install => purecn/create_panel}/environment.yaml (100%) create mode 100644 snappy_wrappers/wrappers/purecn/create_panel/wrapper.py create mode 100644 snappy_wrappers/wrappers/purecn/environment.yaml create mode 120000 snappy_wrappers/wrappers/purecn/prepare/environment.yaml create mode 100644 snappy_wrappers/wrappers/purecn/prepare/wrapper.py create mode 120000 snappy_wrappers/wrappers/purecn/run/environment.yaml create mode 100644 snappy_wrappers/wrappers/purecn/run/wrapper.py create mode 100644 snappy_wrappers/wrappers/r/environment.yaml create mode 100644 snappy_wrappers/wrappers/r/wrapper.py create mode 100644 snappy_wrappers/wrappers/sequenza/environment.yaml create mode 120000 snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml rename snappy_wrappers/wrappers/{scarHRD => sequenza}/gcreference/wrapper.py (80%) create mode 120000 snappy_wrappers/wrappers/sequenza/report/environment.yaml create mode 100644 snappy_wrappers/wrappers/sequenza/report/wrapper.py create mode 120000 snappy_wrappers/wrappers/sequenza/run/environment.yaml create mode 100644 snappy_wrappers/wrappers/sequenza/run/wrapper.py create mode 100644 snappy_wrappers/wrappers/singularity/environment.yaml rename snappy_wrappers/wrappers/{scarHRD/install => singularity}/wrapper.py (56%) diff --git a/snappy_pipeline/apps/snappy_snake.py b/snappy_pipeline/apps/snappy_snake.py index d6ea062f3..edda71f6a 100644 --- a/snappy_pipeline/apps/snappy_snake.py +++ b/snappy_pipeline/apps/snappy_snake.py @@ -32,6 +32,7 @@ ngs_sanity_checking, panel_of_normals, repeat_expansion, + somatic_cnv_checking, somatic_gene_fusion_calling, somatic_hla_loh_calling, somatic_msi_calling, @@ -88,6 +89,7 @@ "panel_of_normals": panel_of_normals, "repeat_analysis": repeat_expansion, "ngs_sanity_checking": ngs_sanity_checking, + "somatic_cnv_checking": somatic_cnv_checking, "somatic_gene_fusion_calling": somatic_gene_fusion_calling, "somatic_hla_loh_calling": somatic_hla_loh_calling, "somatic_msi_calling": somatic_msi_calling, diff --git a/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile b/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile index 92f92482d..fc8dca2ab 100644 --- a/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile +++ b/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile @@ -61,7 +61,12 @@ rule homologous_recombination_deficiency_link_out_run: rule homologous_recombination_deficiency_scarHRD_install: output: **wf.get_output_files("scarHRD", "install"), - threads: wf.get_resource("scarHRD", "install", "threads") + params: + packages=[ + {"name": "aroneklund/copynumber", "repo": "github"}, + {"name": "sequenzatools/sequenza", "repo": "bitbucket"}, + {"name": "sztup/scarHRD", "repo": "github"}, + ], resources: time=wf.get_resource("scarHRD", "install", "time"), memory=wf.get_resource("scarHRD", "install", "memory"), @@ -70,22 +75,7 @@ rule homologous_recombination_deficiency_scarHRD_install: log: **wf.get_log_file("scarHRD", "install"), wrapper: - wf.wrapper_path("scarHRD/install") - - -rule homologous_recombination_deficiency_scarHRD_gcreference: - output: - **wf.get_output_files("scarHRD", "gcreference"), - threads: wf.get_resource("scarHRD", "gcreference", "threads") - resources: - time=wf.get_resource("scarHRD", "gcreference", "time"), - memory=wf.get_resource("scarHRD", "gcreference", "memory"), - partition=wf.get_resource("scarHRD", "gcreference", "partition"), - tmpdir=wf.get_resource("scarHRD", "gcreference", "tmpdir"), - log: - **wf.get_log_file("scarHRD", "gcreference"), - wrapper: - wf.wrapper_path("scarHRD/gcreference") + wf.wrapper_path("r") rule homologous_recombination_deficiency_scarHRD_run: diff --git a/snappy_pipeline/workflows/homologous_recombination_deficiency/__init__.py b/snappy_pipeline/workflows/homologous_recombination_deficiency/__init__.py index bae0d34c6..249fdae69 100644 --- a/snappy_pipeline/workflows/homologous_recombination_deficiency/__init__.py +++ b/snappy_pipeline/workflows/homologous_recombination_deficiency/__init__.py @@ -13,12 +13,17 @@ bioconda directory, while this package is not found when searching `bioconda`. copynumber is obtained from a fork of the official Bioconductor deprecated package. +TODO: The implementation needs to uncouple ``scarHRD`` from ``sequenza``. +It should be possible as ``scarHRD`` could use the output from other CNV callers. +However, it is poorly documented, and will require significant work. + ========== Step Input ========== -``homologous_recombination_deficiency`` starts off the aligned reads, i.e. ``ngs_mapping``. -Both the normal & tumor samples are required to generate the score. +``homologous_recombination_deficiency`` starts off the ``sequenza`` copy number output. +Some steps performed by ``sequenza`` are repeated by ``scanHRD``, as ``scanHRD`` uses a specific +set of arguments. This is the reason why ``sequenza`` is required by the step. =========== Step Output @@ -32,9 +37,9 @@ of this tool. In the future, this section might contain "common" output and tool-specific output sub sections. -- ``{mapper}.scarHRD.{lib_name}-{lib_pk}/out/`` - - ``{mapper}.scarHRD.{lib_name}-{lib_pk}.seqz.gz`` - - ``{mapper}.scarHRD.{lib_name}-{lib_pk}.json`` +- ``{mapper}.{caller}.scarHRD.{lib_name}-{lib_pk}/out/`` + - ``{mapper}.{caller}.scarHRD.{lib_name}-{lib_pk}.seqz.gz`` + - ``{mapper}.{caller}.scarHRD.{lib_name}-{lib_pk}.json`` ===================== Default Configuration @@ -52,7 +57,6 @@ """ -from collections import OrderedDict import sys from biomedsheets.shortcuts import CancerCaseSheet, is_not_background @@ -66,7 +70,9 @@ LinkOutStepPart, ResourceUsage, ) -from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow +from snappy_pipeline.workflows.somatic_targeted_seq_cnv_calling import ( + SomaticTargetedSeqCnvCallingWorkflow, +) __author__ = "Eric Blanc " @@ -75,8 +81,8 @@ # Default configuration homologous_recombination_deficiency step_config: homologous_recombination_deficiency: - tools: ['scarHRD'] # REQUIRED - available: 'mantis' - path_ngs_mapping: ../ngs_mapping # REQUIRED + tools: ['scarHRD'] # REQUIRED - available: 'scarHRD' + path_cnv_calling: ../somatic_targeted_seq_cnv_calling # REQUIRED scarHRD: genome_name: "grch37" # Must be either "grch37", "grch38" or "mouse" chr_prefix: False @@ -93,81 +99,31 @@ class ScarHRDStepPart(BaseStepPart): #: Class available actions actions = ( "install", - "gcreference", "run", ) def __init__(self, parent): super().__init__(parent) - self.base_path_out = ( - "work/{{mapper}}.scarHRD.{{library_name}}/out/{{mapper}}.scarHRD.{{library_name}}{ext}" - ) - # Build shortcut from cancer bio sample name to matched cancer sample - self.tumor_ngs_library_to_sample_pair = OrderedDict() - for sheet in self.parent.shortcut_sheets: - self.tumor_ngs_library_to_sample_pair.update( - sheet.all_sample_pairs_by_tumor_dna_ngs_library - ) - - def get_normal_lib_name(self, wildcards): - """Return name of normal (non-cancer) library""" - pair = self.tumor_ngs_library_to_sample_pair[wildcards.library_name] - return pair.normal_sample.dna_ngs_library.name def get_input_files(self, action): - def input_function_run(wildcards): - """Helper wrapper function""" - # Get shorcut to Snakemake sub workflow - ngs_mapping = self.parent.sub_workflows["ngs_mapping"] - # Get names of primary libraries of the selected cancer bio sample and the - # corresponding primary normal sample - normal_base_path = ( - "output/{mapper}.{normal_library}/out/{mapper}.{normal_library}".format( - normal_library=self.get_normal_lib_name(wildcards), **wildcards - ) - ) - tumor_base_path = ( - "output/{mapper}.{library_name}/out/" "{mapper}.{library_name}" - ).format(**wildcards) - return { - "lib_path": "work/R_packages/out/.done", - "gc": "work/static_data/out/{genome_name}_{length}.wig.gz".format( - genome_name=self.config["scarHRD"]["genome_name"], - length=self.config["scarHRD"]["length"], - ), - "normal_bam": ngs_mapping(normal_base_path + ".bam"), - "normal_bai": ngs_mapping(normal_base_path + ".bam.bai"), - "tumor_bam": ngs_mapping(tumor_base_path + ".bam"), - "tumor_bai": ngs_mapping(tumor_base_path + ".bam.bai"), - } + self._validate_action(action) - if action == "install": - return None - elif action == "gcreference": - return None - elif action == "run": - return input_function_run - else: - raise UnsupportedActionException( - "Action '{action}' is not supported. Valid options: {valid}".format( - action=action, valid=", ".join(self.actions) - ) - ) + return self._get_input_files_run + + @dictify + def _get_input_files_run(self, wildcards): + self.cnv_calling = self.parent.sub_workflows["cnv_calling"] + base_name = f"{wildcards.mapper}.{wildcards.caller}.{wildcards.library_name}" + yield "done", "work/R_packages/out/scarHRD.done" + yield "seqz", self.cnv_calling(f"output/{base_name}/out/{base_name}.seqz.gz") def get_output_files(self, action): if action == "install": - return {"lib_path": "work/R_packages/out/.done"} - elif action == "gcreference": - return { - "gc": "work/static_data/out/{genome_name}_{length}.wig.gz".format( - genome_name=self.config["scarHRD"]["genome_name"], - length=self.config["scarHRD"]["length"], - ) - } + return {"done": "work/R_packages/out/scarHRD.done"} elif action == "run": return { - "sequenza": "work/{mapper}.scarHRD.{library_name}/out/{mapper}.scarHRD.{library_name}.seqz.gz", - "scarHRD": "work/{mapper}.scarHRD.{library_name}/out/{mapper}.scarHRD.{library_name}.json", + "scarHRD": "work/{mapper}.{caller}.scarHRD.{library_name}/out/{mapper}.{caller}.scarHRD.{library_name}.json", + "scarHRD_md5": "work/{mapper}.{caller}.scarHRD.{library_name}/out/{mapper}.{caller}.scarHRD.{library_name}.json.md5", } else: raise UnsupportedActionException( @@ -180,14 +136,9 @@ def get_output_files(self, action): def _get_log_file(self, action): """Return dict of log files.""" if action == "install": - prefix = "work/R_packages/log/R_packages" - elif action == "gcreference": - prefix = "work/static_data/log/{genome_name}_{length}".format( - genome_name=self.config["scarHRD"]["genome_name"], - length=self.config["scarHRD"]["length"], - ) + prefix = "work/R_packages/log/scarHRD" elif action == "run": - prefix = "work/{mapper}.scarHRD.{library_name}/log/{mapper}.scarHRD.{library_name}" + prefix = "work/{mapper}.{caller}.scarHRD.{library_name}/log/{mapper}.{caller}.scarHRD.{library_name}" else: raise UnsupportedActionException( "Action '{action}' is not supported. Valid options: {valid}".format( @@ -204,32 +155,15 @@ def _get_log_file(self, action): yield key + "_md5", prefix + ext + ".md5" def get_resource_usage(self, action): - """Get Resource Usage - - :param action: Action (i.e., step) in the workflow, example: 'run'. - :type action: str - - :return: Returns ResourceUsage for step. - """ - if action == "install" or action == "gcreference": + self._validate_action(action) + if action == "run": return ResourceUsage( threads=1, - time="02:00:00", # 2 hours - memory="4096M", - partition="short", - ) - elif action == "run": - return ResourceUsage( - threads=2, - time="48:00:00", # 2 hours memory="32G", + time="24:00:00", ) else: - raise UnsupportedActionException( - "Action '{action}' is not supported. Valid options: {valid}".format( - action=action, valid=", ".join(self.actions) - ) - ) + return super().get_resource_usage(action) class HomologousRecombinationDeficiencyWorkflow(BaseStep): @@ -253,16 +187,18 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) config_lookup_paths, config_paths, workdir, - (NgsMappingWorkflow,), + (SomaticTargetedSeqCnvCallingWorkflow,), ) # Register sub step classes so the sub steps are available self.register_sub_step_classes((ScarHRDStepPart, LinkOutStepPart)) # Initialize sub-workflows - self.register_sub_workflow("ngs_mapping", self.config["path_ngs_mapping"]) + self.register_sub_workflow( + "somatic_targeted_seq_cnv_calling", self.config["path_cnv_calling"], "cnv_calling" + ) @listify def get_result_files(self): - """Return list of result files for the somatic targeted sequencing CNV calling step""" + """Return list of result files for the homologous recombination deficiency step""" tool_actions = {"scarHRD": ("run",)} for sheet in filter(is_not_background, self.shortcut_sheets): for sample_pair in sheet.all_sample_pairs: @@ -282,14 +218,17 @@ def get_result_files(self): tpls = self.sub_steps[tool].get_output_files(action).values() except AttributeError: tpls = self.sub_steps[tool].get_output_files(action) + tpls = list(tpls) + tpls += list(self.sub_steps[tool].get_log_file(action).values()) for tpl in tpls: filenames = expand( tpl, mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], + caller=["sequenza"], library_name=[sample_pair.tumor_sample.dna_ngs_library.name], ) for f in filenames: - if ".tmp." not in f: + if ".tmp." not in f and not f.endswith(".done"): yield f.replace("work/", "output/") def check_config(self): @@ -298,3 +237,6 @@ def check_config(self): ("static_data_config", "reference", "path"), "Path to reference FASTA file not configured but required", ) + assert ( + "sequenza" in self.w_config["step_config"]["somatic_targeted_seq_cnv_calling"]["tools"] + ) diff --git a/snappy_pipeline/workflows/panel_of_normals/Snakefile b/snappy_pipeline/workflows/panel_of_normals/Snakefile index 427ed25d0..88e132382 100644 --- a/snappy_pipeline/workflows/panel_of_normals/Snakefile +++ b/snappy_pipeline/workflows/panel_of_normals/Snakefile @@ -211,3 +211,69 @@ rule panel_of_normals_cnvkit_report: args=wf.substep_dispatch("cnvkit", "get_args", "report"), wrapper: wf.wrapper_path("cnvkit/report") + + +# Panel of normals (PureCN) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + +# Install the annotation R package -------------------------- + + +rule panel_of_normals_purecn_install: + output: + **wf.get_output_files("purecn", "install"), + params: + container="docker://markusriester/purecn", + resources: + time=wf.get_resource("purecn", "install", "time"), + memory=wf.get_resource("purecn", "install", "memory"), + partition=wf.get_resource("purecn", "install", "partition"), + log: + **wf.get_log_file("purecn", "install"), + wrapper: + wf.wrapper_path("singularity") + + +rule panel_of_normals_purecn_prepare: + input: + **wf.get_input_files("purecn", "prepare"), + output: + **wf.get_output_files("purecn", "prepare"), + resources: + time=wf.get_resource("purecn", "prepare", "time"), + memory=wf.get_resource("purecn", "prepare", "memory"), + partition=wf.get_resource("purecn", "prepare", "partition"), + log: + **wf.get_log_file("purecn", "prepare"), + wrapper: + wf.wrapper_path("purecn/prepare") + + +rule panel_of_normals_purecn_coverage: + input: + unpack(wf.get_input_files("purecn", "coverage")), + output: + **wf.get_output_files("purecn", "coverage"), + resources: + time=wf.get_resource("purecn", "coverage", "time"), + memory=wf.get_resource("purecn", "coverage", "memory"), + partition=wf.get_resource("purecn", "coverage", "partition"), + log: + **wf.get_log_file("purecn", "coverage"), + wrapper: + wf.wrapper_path("purecn/coverage") + + +rule panel_of_normals_purecn_create_panel: + input: + unpack(wf.get_input_files("purecn", "create_panel")), + output: + **wf.get_output_files("purecn", "create_panel"), + resources: + time=wf.get_resource("purecn", "create_panel", "time"), + memory=wf.get_resource("purecn", "create_panel", "memory"), + partition=wf.get_resource("purecn", "create_panel", "partition"), + log: + **wf.get_log_file("purecn", "create_panel"), + wrapper: + wf.wrapper_path("purecn/create_panel") diff --git a/snappy_pipeline/workflows/panel_of_normals/__init__.py b/snappy_pipeline/workflows/panel_of_normals/__init__.py index 3002afedd..63b2921e5 100644 --- a/snappy_pipeline/workflows/panel_of_normals/__init__.py +++ b/snappy_pipeline/workflows/panel_of_normals/__init__.py @@ -105,7 +105,7 @@ __author__ = "Manuel Holtgrewe " #: Names of the tools that might use panel of normals -TOOLS = ["mutect2", "cnvkit", "access"] +TOOLS = ("mutect2", "cnvkit", "access", "purecn") #: Default configuration for the somatic_variant_calling schema DEFAULT_CONFIG = r""" @@ -114,6 +114,9 @@ panel_of_normals: tools: ['mutect2'] # REQUIRED - available: 'mutect2' path_ngs_mapping: ../ngs_mapping # REQUIRED + ignore_chroms: [] # patterns of chromosome names to ignore + # hs37d5: [NC_007605, hs37d5, chrEBV, '*_decoy', 'HLA-*', 'GL000220.*'] + # GRCh38.d1.vd1: [chrEBV, 'HPV*', CMV, HBV, 'HCV-*', 'HIV-*', KSHV, 'HTLV-1', MCV, '*_decoy', 'chrUn_GL00220*', SV40] # Configuration for mutect2 mutect2: path_normals_list: null # Optional file listing libraries to include in panel @@ -134,13 +137,6 @@ job_mult_time: 1 # running time multiplier merge_mult_memory: 1 # memory multiplier for merging merge_mult_time: 1 # running time multiplier for merging - ignore_chroms: # patterns of chromosome names to ignore - - NC_007605 # herpes virus - - hs37d5 # GRCh37 decoy - - chrEBV # Eppstein-Barr Virus - - '*_decoy' # decoy contig - - 'HLA-*' # HLA genes - - 'GL000220.*' # Contig with problematic, repetitive DNA in GRCh37 cnvkit: path_normals_list: "" # Optional file listing libraries to include in panel path_target_regions: "" # Bed files of targetted regions (Missing when creating a panel of normals for WGS data) @@ -163,6 +159,14 @@ access: # Creates access file for cnvkit, based on genomic sequence & excluded regions (optionally) exclude: [] # [access] Bed file of regions to exclude (mappability, blacklisted, ...) min_gap_size: 0 # [access] Minimum gap size between accessible sequence regions (0: use default value) + purecn: + path_normals_list: "" # Optional file listing libraries to include in panel + path_bait_regions: REQUIRED # Bed files of enrichment kit sequences (MergedProbes for Agilent SureSelect), recommended by PureCN author + genome_name: "unknown" # Must be one from hg18, hg19, hg38, mm9, mm10, rn4, rn5, rn6, canFam3 + enrichment_kit_name: "unknown" # For filename only... + mappability: "" # GRCh38: /fast/work/groups/cubi/projects/biotools/static_data/app_support/PureCN/hg38/mappability.bw + reptiming: "" # Nothing for GRCh38 + seed: 1234567 """ @@ -173,13 +177,18 @@ class PanelOfNormalsStepPart(BaseStepPart): merges all the individual results in the the panel. """ - #: Class available actions - actions = ("prepare_panel", "create_panel") + #: Step name (default, must be overwritten) + name = None def __init__(self, parent): super().__init__(parent) # Build shortcut from cancer bio sample name to matched cancer sample self.normal_libraries = list(self._get_normal_libraries()) + if self.name and self.config[self.name].get("path_normals_list"): + self.normal_libraries = [] + with open(self.config[self.name]["path_normals_list"], "rt") as f: + for line in f: + self.normal_libraries.append(line.strip()) def _get_normal_libraries(self): for sheet in self.parent.shortcut_sheets: @@ -193,6 +202,132 @@ def _get_normal_libraries(self): for _, ngs_library in test_sample.ngs_libraries.items(): yield ngs_library.name + @staticmethod + @dictify + def _get_log_file(tpl): + """Return all log files files""" + ext_dict = { + "conda_list": "conda_list.txt", + "conda_list_md5": "conda_list.txt.md5", + "conda_info": "conda_info.txt", + "conda_info_md5": "conda_info.txt.md5", + "log": "log", + "log_md5": "log.md5", + } + for key, ext in ext_dict.items(): + yield key, tpl + "." + ext + + +class PureCnStepPart(PanelOfNormalsStepPart): + """Creating a panel of normals with GC-corrected coverage""" + + #: Step name + name = "purecn" + + #: Actions + actions = ("install", "prepare", "coverage", "create_panel") + + #: Resources + resource_usage = { + "prepare": ResourceUsage( + threads=1, + time="04:00:00", # 4 hours + memory="24G", + ), + "coverage": ResourceUsage( + threads=1, + time="04:00:00", # 4 hours + memory="24G", + ), + "create_panel": ResourceUsage( + threads=1, + time="04:00:00", # 4 hours + memory="24G", + ), + } + + def get_input_files(self, action): + self._validate_action(action) + self.ngs_mapping = self.parent.sub_workflows["ngs_mapping"] + if action == "prepare": + return {"container": "work/containers/out/purecn.simg"} + if action == "coverage": + return self._get_input_files_coverage + if action == "create_panel": + return self._get_input_files_create + + @dictify + def _get_input_files_coverage(self, wildcards): + yield "container", "work/containers/out/purecn.simg" + tpl = "output/{mapper}.{normal_library}/out/{mapper}.{normal_library}.bam" + yield "intervals", "work/purecn/out/{}_{}.list".format( + self.config["purecn"]["enrichment_kit_name"], + self.config["purecn"]["genome_name"], + ) + yield "bam", self.ngs_mapping(tpl.format(**wildcards)) + + @dictify + def _get_input_files_create(self, wildcards): + yield "container", "work/containers/out/purecn.simg" + tpl = "work/{mapper}.purecn/out/{mapper}.{normal_library}_coverage_loess.txt.gz" + yield "normals", [ + tpl.format(mapper=wildcards.mapper, normal_library=lib) for lib in self.normal_libraries + ] + + def get_output_files(self, action): + self._validate_action(action) + + if action == "install": + return {"container": "work/containers/out/purecn.simg"} + if action == "prepare": + base_out = "{}_{}".format( + self.config["purecn"]["enrichment_kit_name"], + self.config["purecn"]["genome_name"], + ) + return { + "intervals": "work/purecn/out/" + base_out + ".list", + "optimized": "work/purecn/out/" + base_out + ".bed.gz", + "tbi": "work/purecn/out/" + base_out + ".bed.gz.tbi", + "intervals_md5": "work/purecn/out/" + base_out + ".list.md5", + "optimized_md5": "work/purecn/out/" + base_out + ".bed.gz.md5", + "tbi_md5": "work/purecn/out/" + base_out + ".bed.gz.tbi.md5", + } + if action == "coverage": + return { + "coverage": "work/{mapper}.purecn/out/{mapper}.{normal_library,.+-DNA[0-9]+-WES[0-9]+}_coverage_loess.txt.gz" + } + if action == "create_panel": + return { + "db": "work/{mapper}.purecn/out/{mapper}.purecn.panel_of_normals.rds", + "db_md5": "work/{mapper}.purecn/out/{mapper}.purecn.panel_of_normals.rds.md5", + "mapbias": "work/{mapper}.purecn/out/{mapper}.purecn.mapping_bias.rds", + "mapbias_md5": "work/{mapper}.purecn/out/{mapper}.purecn.mapping_bias.rds.md5", + "lowcov": "work/{mapper}.purecn/out/{mapper}.purecn.low_coverage_targets.bed", + "hq": "work/{mapper}.purecn/out/{mapper}.purecn.hq_sites.bed", + "plot": "work/{mapper}.purecn/out/{mapper}.purecn.interval_weights.png", + } + + def get_log_file(self, action): + tpls = { + "install": "work/containers/log/purecn", + "prepare": "work/purecn/log/{}_{}".format( + self.config["purecn"]["enrichment_kit_name"], + self.config["purecn"]["genome_name"], + ), + "coverage": "work/{mapper}.purecn/log/{mapper}.{normal_library,.+-DNA[0-9]+-WES[0-9]+}", + "create_panel": "work/{mapper}.purecn/log/{mapper}.purecn.panel_of_normals", + } + assert action in self.actions + return self._get_log_file(tpls[action]) + + def check_config(self): + if self.name not in self.config["tools"]: + return # PureCN not enabled, skip + self.parent.ensure_w_config( + ("step_config", "panel_of_normals", self.name, "path_bait_regions"), + "Path to exome panel bait regions not defined for tool {}".format(self.name), + ) + class Mutect2StepPart(PanelOfNormalsStepPart): """Somatic variant calling with MuTect 2""" @@ -200,8 +335,11 @@ class Mutect2StepPart(PanelOfNormalsStepPart): #: Step name name = "mutect2" + #: Class available actions + actions = ("prepare_panel", "create_panel") + #: Class resource usage dictionary. Key: action type (string); Value: resource (ResourceUsage). - resource_usage_dict = { + resource_usage = { "prepare_panel": ResourceUsage( threads=2, time="3-00:00:00", # 3 days @@ -214,14 +352,6 @@ class Mutect2StepPart(PanelOfNormalsStepPart): ), } - def __init__(self, parent): - super().__init__(parent) - if self.config["mutect2"]["path_normals_list"]: - self.normal_libraries = [] - with open(self.config["mutect2"]["path_normals_list"], "rt") as f: - for line in f: - self.normal_libraries.append(line.strip()) - def check_config(self): if self.name not in self.config["tools"]: return # Mutect not enabled, skip @@ -230,18 +360,6 @@ def check_config(self): "Path to reference FASTA not configured but required for %s" % (self.name,), ) - def get_resource_usage(self, action): - """Get Resource Usage - - :param action: Action (i.e., step) in the workflow, example: 'run'. - :type action: str - - :return: Returns ResourceUsage for step. - """ - # Validate action - self._validate_action(action) - return self.resource_usage_dict.get(action) - def get_input_files(self, action): """Return input files for mutect2 variant calling""" # Validate action @@ -279,30 +397,24 @@ def get_output_files(self, action): "vcf_tbi_md5": "vcf.gz.tbi.md5", } tpls = { - "prepare_panel": "work/{{mapper}}.{tool}/out/{{mapper}}.{tool}.{{normal_library}}.prepare.{ext}", - "create_panel": "work/{{mapper}}.{tool}/out/{{mapper}}.{tool}.panel_of_normals.{ext}", + "prepare_panel": "work/{mapper}.mutect2/out/{mapper}.mutect2.{normal_library}.prepare", + "create_panel": "work/{mapper}.mutect2/out/{mapper}.mutect2.panel_of_normals", } for key, ext in ext_dict.items(): - yield key, tpls[action].format(tool=self.name, ext=ext) + yield key, tpls[action] + "." + ext + if action == "create_panel": + yield "db", "work/{mapper}.mutect2/out/{mapper}.mutect2.genomicsDB.tar.gz" + yield "db_md5", "work/{mapper}.mutect2/out/{mapper}.mutect2.genomicsDB.tar.gz.md5" - @dictify - def get_log_file(self, action): + @classmethod + def get_log_file(cls, action): """Return panel of normal files""" - self._validate_action(action) - ext_dict = { - "conda_list": "conda_list.txt", - "conda_list_md5": "conda_list.txt.md5", - "conda_info": "conda_info.txt", - "conda_info_md5": "conda_info.txt.md5", - "log": "log", - "log_md5": "log.md5", - } tpls = { - "prepare_panel": "work/{{mapper}}.{tool}/log/{{mapper}}.{tool}.{{normal_library}}.prepare.{ext}", - "create_panel": "work/{{mapper}}.{tool}/log/{{mapper}}.{tool}.panel_of_normals.{ext}", + "prepare_panel": "work/{mapper}.mutect2/log/{mapper}.mutect2.{normal_library}.prepare", + "create_panel": "work/{mapper}.mutect2/log/{mapper}.mutect2.panel_of_normals", } - for key, ext in ext_dict.items(): - yield key, tpls[action].format(tool=self.name, ext=ext) + assert action in cls.actions + return cls._get_log_file(tpls[action]) class CnvkitStepPart(PanelOfNormalsStepPart): @@ -321,7 +433,7 @@ class CnvkitStepPart(PanelOfNormalsStepPart): ) #: Class resource usage dictionary. Key: action type (string); Value: resource (ResourceUsage). - resource_usage_dict = { + resource_usage = { "target": ResourceUsage( threads=2, time="02:00:00", # 2 hours @@ -351,11 +463,6 @@ class CnvkitStepPart(PanelOfNormalsStepPart): def __init__(self, parent): super().__init__(parent) - if self.config["cnvkit"]["path_normals_list"]: - self.normal_libraries = [] - with open(self.config["cnvkit"]["path_normals_list"], "rt") as f: - for line in f: - self.normal_libraries.append(line.strip()) self.is_wgs = self.config["cnvkit"]["path_target_regions"] == "" def check_config(self): @@ -374,18 +481,6 @@ def get_args(self, action): method = "hybrid" return {"method": method, "flat": (len(self.normal_libraries) == 0)} - def get_resource_usage(self, action): - """Get Resource Usage - - :param action: Action (i.e., step) in the workflow, example: 'run'. - :type action: str - - :return: Returns ResourceUsage for step. - """ - # Validate action - self._validate_action(action) - return self.resource_usage_dict.get(action) - def get_input_files(self, action): """Return input files for cnvkit panel of normals creation""" # Validate action @@ -527,33 +622,19 @@ def _get_output_files_access(self): "access_md5": "work/cnvkit.access/out/cnvkit.access.bed.md5", } - @dictify - def get_log_file(self, action): + @classmethod + def get_log_file(cls, action): """Return panel of normal files""" - ext_dict = { - "conda_list": "conda_list.txt", - "conda_list_md5": "conda_list.txt.md5", - "conda_info": "conda_info.txt", - "conda_info_md5": "conda_info.txt.md5", - "log": "log", - "log_md5": "log.md5", + tpls = { + "target": "work/{mapper}.cnvkit/log/{mapper}.cnvkit.target", + "antitarget": "work/{mapper}.cnvkit/log/{mapper}.cnvkit.antitarget", + "coverage": "work/{mapper}.cnvkit/log/{mapper}.cnvkit.{normal_library}.coverage", + "create_panel": "work/{mapper}.cnvkit/log/{mapper}.cnvkit.panel_of_normals", + "report": "work/{mapper}.cnvkit/log/{mapper}.cnvkit.report", + "access": "work/cnvkit.access/log/cnvkit.access", } - if action == "target": - tpl = "work/{{mapper}}.cnvkit/log/{{mapper}}.cnvkit.target.{ext}" - elif action == "antitarget": - tpl = "work/{{mapper}}.cnvkit/log/{{mapper}}.cnvkit.antitarget.{ext}" - elif action == "coverage": - tpl = "work/{{mapper}}.cnvkit/log/{{mapper}}.cnvkit.{{normal_library}}.coverage.{ext}" - elif action == "create_panel": - tpl = "work/{{mapper}}.cnvkit/log/{{mapper}}.cnvkit.panel_of_normals.{ext}" - elif action == "report": - tpl = "work/{{mapper}}.cnvkit/log/{{mapper}}.cnvkit.report.{ext}" - elif action == "access": - tpl = "work/cnvkit.access/log/cnvkit.access.{ext}" - else: - self._validate_action(action) - for key, ext in ext_dict.items(): - yield key, tpl.format(ext=ext) + assert action in cls.actions + return cls._get_log_file(tpls[action]) class AccessStepPart(PanelOfNormalsStepPart): @@ -582,22 +663,11 @@ def get_output_files(self, action): tpl = "work/cnvkit.access/out/cnvkit.access.bed" return {"access": tpl, "access_md5": tpl + ".md5"} - @dictify - def get_log_file(self, action): + @classmethod + def get_log_file(cls, action): """Return log files""" - # Validate action - self._validate_action(action) - ext_dict = { - "conda_list": "conda_list.txt", - "conda_list_md5": "conda_list.txt.md5", - "conda_info": "conda_info.txt", - "conda_info_md5": "conda_info.txt.md5", - "log": "log", - "log_md5": "log.md5", - } - tpl = "work/cnvkit.access/log/cnvkit.access.{ext}" - for key, ext in ext_dict.items(): - yield key, tpl.format(ext=ext) + assert action in cls.actions + return cls._get_log_file("work/cnvkit.access/log/cnvkit.access") class PanelOfNormalsWorkflow(BaseStep): @@ -627,17 +697,18 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) workdir, (NgsMappingWorkflow,), ) + # Initialize sub-workflows + self.register_sub_workflow("ngs_mapping", self.config["path_ngs_mapping"]) # Register sub step classes so the sub steps are available self.register_sub_step_classes( ( Mutect2StepPart, CnvkitStepPart, AccessStepPart, + PureCnStepPart, LinkOutStepPart, ) ) - # Initialize sub-workflows - self.register_sub_workflow("ngs_mapping", self.config["path_ngs_mapping"]) @listify def get_result_files(self): @@ -660,6 +731,9 @@ def get_result_files(self): tpl = "output/{mapper}.mutect2/out/{mapper}.mutect2.panel_of_normals.{ext}" ext_list = ("vcf.gz", "vcf.gz.md5", "vcf.gz.tbi", "vcf.gz.tbi.md5") result_files.extend(self._expand_result_files(tpl, ext_list)) + tpl = "output/{mapper}.mutect2/out/{mapper}.mutect2.genomicsDB.{ext}" + ext_list = ("tar.gz", "tar.gz.md5") + result_files.extend(self._expand_result_files(tpl, ext_list)) tpl = "output/{mapper}.mutect2/log/{mapper}.mutect2.panel_of_normals.{ext}" result_files.extend(self._expand_result_files(tpl, log_ext_list)) @@ -697,6 +771,27 @@ def get_result_files(self): tpl = "output/cnvkit.access/log/cnvkit.access.{ext}" result_files.extend(self._expand_result_files(tpl, log_ext_list)) + if "purecn" in set(self.config["tools"]) & set(TOOLS): + tpl = "output/{mapper}.purecn/out/{mapper}.purecn.panel_of_normals.{ext}" + ext_list = ("rds", "rds.md5") + result_files.extend(self._expand_result_files(tpl, ext_list)) + tpl = "output/{mapper}.purecn/out/{mapper}.purecn.mapping_bias.{ext}" + ext_list = ("rds", "rds.md5") + result_files.extend(self._expand_result_files(tpl, ext_list)) + tpl = "output/{mapper}.purecn/log/{mapper}.purecn.panel_of_normals.{ext}" + result_files.extend(self._expand_result_files(tpl, log_ext_list)) + tpl = "output/purecn/out/{}_{}.{{ext}}".format( + self.config["purecn"]["enrichment_kit_name"], + self.config["purecn"]["genome_name"], + ) + ext_list = ("list", "list.md5", "bed.gz", "bed.gz.md5", "bed.gz.tbi", "bed.gz.tbi.md5") + result_files.extend(self._expand_result_files(tpl, ext_list)) + tpl = "output/purecn/log/{}_{}.{{ext}}".format( + self.config["purecn"]["enrichment_kit_name"], + self.config["purecn"]["genome_name"], + ) + result_files.extend(self._expand_result_files(tpl, log_ext_list)) + return result_files def _expand_result_files(self, tpl, ext_list): diff --git a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/Snakefile b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/Snakefile index 91d449628..330476306 100644 --- a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/Snakefile +++ b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/Snakefile @@ -233,3 +233,113 @@ rule somatic_targeted_seq_cnv_calling_cnvetti_off_target_postprocess: **wf.get_log_file("cnvetti_off_target", "postprocess"), wrapper: wf.wrapper_path("cnvetti/on_target/postprocess") + + +# Run sequenza ---------------------------------------------------- + + +rule somatic_targeted_seq_cnv_calling_sequenza_install: + output: + **wf.get_output_files("sequenza", "install"), + params: + packages=[ + {"name": "aroneklund/copynumber", "repo": "github"}, + ], + threads: wf.get_resource("sequenza", "install", "threads") + resources: + time=wf.get_resource("sequenza", "install", "time"), + memory=wf.get_resource("sequenza", "install", "memory"), + partition=wf.get_resource("sequenza", "install", "partition"), + tmpdir=wf.get_resource("sequenza", "install", "tmpdir"), + log: + **wf.get_log_file("sequenza", "install"), + wrapper: + wf.wrapper_path("r") + + +rule somatic_targeted_seq_cnv_calling_sequenza_gcreference: + output: + **wf.get_output_files("sequenza", "gcreference"), + threads: wf.get_resource("sequenza", "gcreference", "threads") + resources: + time=wf.get_resource("sequenza", "gcreference", "time"), + memory=wf.get_resource("sequenza", "gcreference", "memory"), + partition=wf.get_resource("sequenza", "gcreference", "partition"), + tmpdir=wf.get_resource("sequenza", "gcreference", "tmpdir"), + log: + **wf.get_log_file("sequenza", "gcreference"), + wrapper: + wf.wrapper_path("sequenza/gcreference") + + +rule somatic_targeted_seq_cnv_calling_sequenza_run: + input: + unpack(wf.get_input_files("sequenza", "run")), + output: + **wf.get_output_files("sequenza", "run"), + threads: wf.get_resource("sequenza", "run", "threads") + resources: + time=wf.get_resource("sequenza", "run", "time"), + memory=wf.get_resource("sequenza", "run", "memory"), + partition=wf.get_resource("sequenza", "run", "partition"), + tmpdir=wf.get_resource("sequenza", "run", "tmpdir"), + log: + **wf.get_log_file("sequenza", "run"), + wrapper: + wf.wrapper_path("sequenza/run") + + +rule somatic_targeted_seq_cnv_calling_sequenza_report: + input: + **wf.get_input_files("sequenza", "report"), + output: + **wf.get_output_files("sequenza", "report"), + params: + sample_id=wf.get_params("sequenza", "report"), + threads: wf.get_resource("sequenza", "report", "threads") + resources: + time=wf.get_resource("sequenza", "report", "time"), + memory=wf.get_resource("sequenza", "report", "memory"), + partition=wf.get_resource("sequenza", "report", "partition"), + tmpdir=wf.get_resource("sequenza", "report", "tmpdir"), + log: + **wf.get_log_file("sequenza", "report"), + wrapper: + wf.wrapper_path("sequenza/report") + + +# Run PureCN ------------------------------------------------------ + + +rule somatic_targeted_seq_cnv_calling_purecn_coverage: + input: + unpack(wf.get_input_files("purecn", "coverage")), + output: + **wf.get_output_files("purecn", "coverage"), + threads: wf.get_resource("purecn", "coverage", "threads") + resources: + time=wf.get_resource("purecn", "coverage", "time"), + memory=wf.get_resource("purecn", "coverage", "memory"), + partition=wf.get_resource("purecn", "coverage", "partition"), + tmpdir=wf.get_resource("purecn", "coverage", "tmpdir"), + log: + **wf.get_log_file("purecn", "coverage"), + wrapper: + wf.wrapper_path("purecn/coverage") + + +rule somatic_targeted_seq_cnv_calling_purecn_run: + input: + unpack(wf.get_input_files("purecn", "run")), + output: + **wf.get_output_files("purecn", "run"), + threads: wf.get_resource("purecn", "run", "threads") + resources: + time=wf.get_resource("purecn", "run", "time"), + memory=wf.get_resource("purecn", "run", "memory"), + partition=wf.get_resource("purecn", "run", "partition"), + tmpdir=wf.get_resource("purecn", "run", "tmpdir"), + log: + **wf.get_log_file("purecn", "run"), + wrapper: + wf.wrapper_path("purecn/run") diff --git a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py index 4f80a78c5..91d708894 100644 --- a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py +++ b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py @@ -104,6 +104,7 @@ from biomedsheets.shortcuts import CancerCaseSheet, CancerCaseSheetOptions, is_not_background from snakemake.io import expand +from snappy_pipeline.base import UnsupportedActionException from snappy_pipeline.utils import dictify, listify from snappy_pipeline.workflows.abstract import ( BaseStep, @@ -120,7 +121,7 @@ # Default configuration somatic_targeted_seq_cnv_calling step_config: somatic_targeted_seq_cnv_calling: - tools: ['cnvkit'] # REQUIRED - available: 'cnvkit', 'copywriter', 'cnvetti_on_target' and 'cnvetti_off_target' + tools: ['cnvkit'] # REQUIRED - available: 'cnvkit', 'sequenza', 'cnvetti_on_target', 'cnvetti_off_target' and 'copywriter' (deprecated) path_ngs_mapping: ../ngs_mapping # REQUIRED cnvkit: path_target: REQUIRED # Usually ../panel_of_normals/output/cnvkit.target/out/cnvkit.target.bed @@ -162,6 +163,27 @@ segmetrics_alpha: 0.05 # [segmetrics] Significance cutoff segmetrics_bootstrap: 100 # [segmetrics] Number of bootstraps smooth_bootstrap: False # [segmetrics] Smooth bootstrap results + sequenza: + length: 50 + assembly: "hg19" # Must be hg38 for GRCh38. See copynumber for complete list (augmented with hg38) + extra_args: {} # Extra arguments for sequenza bam2seqz, valid values: + # hom: 0.9 # Threshold to select homozygous positions + # het: 0.25 # Threshold to select heterozygous positions + # qlimit: 20 # Minimum nucleotide quality score for inclusion in the counts + # qformat: "sanger" # Quality format, options are "sanger" or "illumina". This will add an offset of 33 or 64 respectively to the qlimit value + ignore_chroms: # patterns of chromosome names to ignore + [X, Y, MT, NC_007605. hs37d5, chrEBV, '*_decoy', 'HLA-*', 'GL000220.*'] # Genome hs37d5 + # [chrX, chrY, chrM, '*_random', 'chrUn_*', chrEBV, '*_decoy', 'HPV*', CMV, HBV, KSHV, MCV, SV40, 'HCV-*', 'HIV-*', 'HTLV-*'] # Genome GRch38.d1.vd1 + extra_args_extract: # Valid arguments: see ?sequenza::sequenza.extract in R + gamma: 60 # scarHRD value + kmin: 50 # scarHRD value + extra_args_fit: # Valid arguments: see ?sequenza::sequenza.fit in R + N.ratio.filter: 10 # scarHRD value + N.BAF.filter: 1 # scarHRD value + segment.filter: 3000000 # scarHRD value + mufreq.treshold: 0.1 # scarHRD value + ratio.priority: False # scarHRD value + ploidy: [1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5] copywriter: path_target_regions: REQUIRED # REQUIRED bin_size: 20000 # TODO: make actually configurable @@ -170,6 +192,24 @@ features: EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75 prefix: '' nThread: 8 + purecn: + genome_name: "unknown" # Must be one from hg18, hg19, hg38, mm9, mm10, rn4, rn5, rn6, canFam3 + enrichment_kit_name: "unknown" # For filename only... + mappability: "" # GRCh38: /fast/work/groups/cubi/projects/biotools/static_data/app_support/PureCN/hg38/mappability.bw + reptiming: "" # Nothing for GRCh38 + seed: 1234567 + extra_commands: # Recommended extra arguments for PureCN, extra_arguments: [] to clear them all + model: betabin + "fun-segmentation": PSCBS + "post-optimize": "" # post-optimize is a flag + # A PureCN panel of normals is required, with the container, the intervals & the PON rds file + path_container: REQUIRED # ../panel_of_normals/work/containers/out/purecn.simg + path_intervals: REQUIRED # ../panel_of_normals/output/purecn/out/_.list + path_panel_of_normals: REQUIRED # ../panel_of_normals/output/bwa.purecn/out/bwa.purecn.panel_of_normals.rds + path_mapping_bias: REQUIRED # ../panel_of_normals/output/bwa.purecn/out/bwa.purecn.mapping_bias.rds + # IMPORTANT NOTE: Mutect2 must be called with "--genotype-germline-sites true --genotype-pon-sites true" + somatic_variant_caller: "mutect2" + path_somatic_variants: ../somatic_variant_calling_for_purecn cnvetti_on_target: path_target_regions: REQUIRED # REQUIRED cnvetti_off_target: @@ -215,6 +255,18 @@ def get_normal_lib_name(self, wildcards): pair = self.tumor_ngs_library_to_sample_pair[wildcards.library_name] return pair.normal_sample.dna_ngs_library.name + @staticmethod + @dictify + def _get_log_file_from_prefix(prefix): + key_ext = ( + ("log", ".log"), + ("conda_info", ".conda_info.txt"), + ("conda_list", ".conda_list.txt"), + ) + for key, ext in key_ext: + yield key, prefix + ext + yield key + "_md5", prefix + ext + ".md5" + class CnvettiStepPartBase(SomaticTargetedSeqCnvCallingStepPart): """Perform somatic targeted CNV calling using CNVetti; shared code. @@ -351,19 +403,13 @@ def check_config(self): "Path to target regions is missing for {}".format(self.name), ) - @dictify def _get_log_file(self, action): """Return path to log file for the given action""" # Validate action self._validate_action(action) name_pattern = self.name_pattern.format(action=action) - key_ext = ( - ("log", ".log"), - ("conda_info", ".conda_info.txt"), - ("conda_list", ".conda_list.txt"), - ) - for key, ext in key_ext: - yield key, os.path.join("work", name_pattern, "log", name_pattern + ext) + prefix = os.path.join("work", name_pattern, "log", name_pattern) + return self._get_log_file_from_prefix(prefix) def get_resource_usage(self, action): """Get Resource Usage @@ -420,6 +466,225 @@ def format_id(*args): return {key: "{{{}}}".format(key) for key in args} +class SequenzaStepPart(SomaticTargetedSeqCnvCallingStepPart): + """Perform somatic targeted CNV calling using sequenza""" + + #: Step name + name = "sequenza" + + #: Class available actions + actions = ( + "install", + "gcreference", + "run", + "report", + ) + + #: Class resource usage dictionary. Key: action type (string); Value: resource (ResourceUsage). + resource_usage = { + "run": ResourceUsage( + threads=4, + time="24:00:00", # 1 day + memory="16G", + ), + } + + def __init__(self, parent): + super().__init__(parent) + + def get_input_files(self, action): + """Return input paths input function, dependent on rule""" + # Validate action + self._validate_action(action) + + method_mapping = { + "run": self._get_input_files_run(), + "report": self._get_input_files_report(), + } + return method_mapping[action] + + def _get_input_files_run(self): + @dictify + def input_function(wildcards): + ngs_mapping = self.parent.sub_workflows["ngs_mapping"] + normal_base_path = ( + "output/{mapper}.{normal_library}/out/{mapper}.{normal_library}".format( + normal_library=self.get_normal_lib_name(wildcards), **wildcards + ) + ) + tumor_base_path = "output/{mapper}.{library_name}/out/{mapper}.{library_name}".format( + **wildcards + ) + yield "gc", "work/static_data/out/sequenza.{length}.wig.gz".format( + length=self.config["sequenza"]["length"], + ) + yield "normal_bam", ngs_mapping(normal_base_path + ".bam") + yield "normal_bai", ngs_mapping(normal_base_path + ".bam.bai") + yield "tumor_bam", ngs_mapping(tumor_base_path + ".bam") + yield "tumor_bai", ngs_mapping(tumor_base_path + ".bam.bai") + + return input_function + + def _get_input_files_report(self): + return { + "packages": "work/R_packages/out/sequenza.done", + "seqz": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz", + } + + def get_output_files(self, action): + if action == "install": + return {"done": "work/R_packages/out/sequenza.done"} + elif action == "gcreference": + return { + "gc": "work/static_data/out/sequenza.{length}.wig.gz".format( + length=self.config["sequenza"]["length"], + ) + } + elif action == "run": + return { + "seqz": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz", + "seqz_md5": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz.md5", + } + elif action == "report": + return {"done": "work/{mapper}.sequenza.{library_name}/report/.done"} + else: + raise UnsupportedActionException( + "Action '{action}' is not supported. Valid options: {valid}".format( + action=action, valid=", ".join(self.actions) + ) + ) + + def get_params(self, action): + self._validate_action(action) + return self._get_params_report + + def _get_params_report(self, wildcards): + return wildcards["library_name"] + + def get_log_file(self, action): + """Return dict of log files.""" + # Validate action + self._validate_action(action) + if action == "install": + prefix = "work/R_packages/log/sequenza" + elif action == "gcreference": + prefix = "work/static_data/log/sequenza.{length}".format( + length=self.config["sequenza"]["length"], + ) + else: + name_pattern = "{mapper}.sequenza.{library_name}" + prefix = os.path.join("work", name_pattern, "log", name_pattern + "." + action) + return self._get_log_file_from_prefix(prefix) + + +class PureCNStepPart(SomaticTargetedSeqCnvCallingStepPart): + """Perform somatic targeted CNV calling using PureCN""" + + #: Step name + name = "purecn" + + #: Class available actions + actions = ("coverage", "run") + + resource_usage = { + "coverage": ResourceUsage( + threads=1, + time="04:00:00", # 4 hours + memory="24G", + ), + "run": ResourceUsage( + threads=4, + time="24:00:00", # 4 hours + memory="96G", + ), + } + + def get_input_files(self, action): + """Return input paths input function, dependent on rule""" + # Validate action + self._validate_action(action) + action_mapping = { + "coverage": self._get_input_files_coverage, + "run": self._get_input_files_run, + } + return action_mapping[action] + + @dictify + def _get_input_files_run(self, wildcards): + name_pattern = "{mapper}.purecn.{library_name}".format(**wildcards) + yield "tumor", os.path.join( + "work", + name_pattern, + "out", + "{mapper}.{library_name}_coverage_loess.txt.gz".format(**wildcards), + ) + name_pattern = "{mapper}.{caller}.{library_name}".format( + caller=self.config["purecn"]["somatic_variant_caller"], + **wildcards, + ) + base_path = os.path.join("output", name_pattern, "out", name_pattern + ".full.vcf.gz") + variant_calling = self.parent.sub_workflows["somatic_variants"] + yield "vcf", variant_calling(base_path) + + @dictify + def _get_input_files_coverage(self, wildcards): + ngs_mapping = self.parent.sub_workflows["ngs_mapping"] + name_pattern = "{mapper}.{library_name}".format(**wildcards) + base_path = os.path.join("output", name_pattern, "out", name_pattern) + yield "bam", ngs_mapping(base_path + ".bam") + yield "bai", ngs_mapping(base_path + ".bam.bai") + + def get_output_files(self, action): + """Return output paths, dependent on rule""" + # Validate action + self._validate_action(action) + name_pattern = "{mapper}.purecn.{library_name}" + prefix = os.path.join("work", name_pattern, "out", "{library_name}") + action_mapping = { + "coverage": { + "coverage": os.path.join( + "work", name_pattern, "out", "{mapper}.{library_name}_coverage_loess.txt.gz" + ) + }, + "run": { + "segments": prefix + "_dnacopy.seg", + "ploidy": prefix + ".csv", + "pvalues": prefix + "_amplification_pvalues.csv", + "vcf": prefix + ".vcf.gz", + "vcf_tbi": prefix + ".vcf.gz.tbi", + "loh": prefix + "_loh.csv", + "segments_md5": prefix + "_dnacopy.seg.md5", + "ploidy_md5": prefix + ".csv.md5", + "pvalues_md5": prefix + "_amplification_pvalues.csv.md5", + "vcf_md5": prefix + ".vcf.gz.md5", + "vcf_tbi_md5": prefix + ".vcf.gz.tbi.md5", + "loh_md5": prefix + "_loh.csv.md5", + }, + } + return action_mapping[action] + + def get_log_file(self, action): + """Return dict of log files.""" + # Validate action + self._validate_action(action) + + name_pattern = "{mapper}.purecn.{library_name}" + prefix = os.path.join("work", name_pattern, "log", name_pattern + "." + action) + return self._get_log_file_from_prefix(prefix) + + def check_config(self): + if self.name not in self.config["tools"]: + return # skip check + self.parent.ensure_w_config( + ("step_config", "somatic_targeted_seq_cnv_calling", self.name, "path_panel_of_normals"), + "Path to the PureCN panel of normal is missing", + ) + self.parent.ensure_w_config( + ("step_config", "somatic_targeted_seq_cnv_calling", self.name, "path_mapping_bias"), + "Path to the PureCN mapping bias file is missing (created in the panel_of_normals step)", + ) + + class CnvKitStepPart(SomaticTargetedSeqCnvCallingStepPart): """Perform somatic targeted CNV calling using cnvkit""" @@ -438,8 +703,11 @@ class CnvKitStepPart(SomaticTargetedSeqCnvCallingStepPart): "report", ) + # Overwrite defaults + default_resource_usage = ResourceUsage(threads=1, time="03:59:59", memory="7680M") # 4h + #: Class resource usage dictionary. Key: action type (string); Value: resource (ResourceUsage). - resource_usage_dict = { + resource_usage = { "plot": ResourceUsage( threads=1, time="08:00:00", # 1 day @@ -450,11 +718,6 @@ class CnvKitStepPart(SomaticTargetedSeqCnvCallingStepPart): time="08:00:00", # 8 hours memory=f"{16 * 1024}M", ), - "default": ResourceUsage( - threads=1, - time="03:59:59", # 1 day - memory=f"{int(7.5 * 1024)}M", - ), } def __init__(self, parent): @@ -689,33 +952,7 @@ def get_log_file(self, action): "work/{{mapper}}.cnvkit.{{library_name}}/log/" "{{mapper}}.cnvkit.{action}.{{library_name}}" ).format(action=action) - key_ext = ( - ("log", ".log"), - ("conda_info", ".conda_info.txt"), - ("conda_list", ".conda_list.txt"), - ) - log_files = {} - for key, ext in key_ext: - log_files[key] = prefix + ext - log_files[key + "_md5"] = prefix + ext + ".md5" - return log_files - - def get_resource_usage(self, action): - """Get Resource Usage - - :param action: Action (i.e., step) in the workflow, example: 'run'. - :type action: str - - :return: Returns ResourceUsage for step. - """ - # Validate action - self._validate_action(action) - if action == "plot": - return self.resource_usage_dict.get("plot") - elif action == "coverage": - return self.resource_usage_dict.get("coverage") - else: - return self.resource_usage_dict.get("default") + return self._get_log_file_from_prefix(prefix) class CopywriterStepPart(SomaticTargetedSeqCnvCallingStepPart): @@ -731,7 +968,7 @@ class CopywriterStepPart(SomaticTargetedSeqCnvCallingStepPart): actions_w_in_out = ("run", "call") #: Class resource usage dictionary. Key: action type (string); Value: resource (ResourceUsage). - resource_usage_dict = { + resource_usage = { "prepare": ResourceUsage( threads=1, time="02:00:00", # 2 hours @@ -844,41 +1081,18 @@ def check_config(self): "Path to target regions is missing", ) - @dictify - def _get_log_file(self, action): + def get_log_file(self, action): """Return path to log file for the given action""" # Validate action self._validate_action(action) - key_ext = ( - ("log", ".log"), - ("conda_info", ".conda_info.txt"), - ("conda_list", ".conda_list.txt"), - ) - if action == "prepare": log_file = "work/copywriter.prepare/log/snakemake.log" - yield "log", log_file - yield "log_md5", log_file + ".md5" - elif action in ("call", "run"): - tpl = ( - "work/{mapper}.copywriter.{library_name}/log/{mapper}.copywriter.{library_name}." - + action - ) - for key, ext in key_ext: - yield key, tpl + ext - - def get_resource_usage(self, action): - """Get Resource Usage - - :param action: Action (i.e., step) in the workflow, example: 'run'. - :type action: str - - :return: Returns ResourceUsage for step. - """ - # Validate action - self._validate_action(action) - return self.resource_usage_dict.get(action) + return {"log": log_file, "log_md5": log_file + ".md5"} + else: + name_pattern = "{mapper}.copywriter.{library_name}" + prefix = os.path.join("work", name_pattern, "log", name_pattern + "." + action) + return self._get_log_file_from_prefix(prefix) class SomaticTargetedSeqCnvCallingWorkflow(BaseStep): @@ -915,17 +1129,27 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) CnvettiOnTargetStepPart, CnvKitStepPart, CopywriterStepPart, + SequenzaStepPart, + PureCNStepPart, LinkOutStepPart, ) ) # Initialize sub-workflows self.register_sub_workflow("ngs_mapping", self.config["path_ngs_mapping"]) + if "purecn" in self.config["tools"]: + self.register_sub_workflow( + "somatic_variant_calling", + self.config["purecn"]["path_somatic_variants"], + "somatic_variants", + ) @listify def get_result_files(self): """Return list of result files for the somatic targeted sequencing CNV calling step""" tool_actions = { "cnvkit": ["fix", "postprocess", "report", "export"], + "sequenza": ("run",), + "purecn": ("run",), "copywriter": ("call",), "cnvetti_on_target": ("coverage", "segment", "postprocess"), "cnvetti_off_target": ("coverage", "segment", "postprocess"), @@ -951,7 +1175,7 @@ def get_result_files(self): except AttributeError: tpls = [self.sub_steps[tool].get_output_files(action)] try: - tpls += self.sub_steps[tool].get_log_file(action).values() + tpls += list(self.sub_steps[tool].get_log_file(action).values()) except AttributeError: tpls += [self.sub_steps[tool].get_log_file(action)] for tpl in tpls: @@ -961,7 +1185,7 @@ def get_result_files(self): library_name=[sample_pair.tumor_sample.dna_ngs_library.name], ) for f in filenames: - if ".tmp." not in f: + if ".tmp." not in f and not f.endswith("/.done"): yield f.replace("work/", "output/") def check_config(self): diff --git a/snappy_wrappers/wrappers/mutect2/create_panel/wrapper.py b/snappy_wrappers/wrappers/mutect2/create_panel/wrapper.py index 8c3742c00..a800cf953 100644 --- a/snappy_wrappers/wrappers/mutect2/create_panel/wrapper.py +++ b/snappy_wrappers/wrappers/mutect2/create_panel/wrapper.py @@ -50,6 +50,7 @@ mkdir -p ${{tmpdir}}/vcfs out_base=${{tmpdir}}/out/$(basename {snakemake.output.vcf} .vcf.gz) +mkdir -p $out_base vcfs=$(echo "{snakemake.input.normals}" | tr ' ' '\n') @@ -67,7 +68,7 @@ sort ${{tmpdir}}/contigs_all.list | uniq > ${{tmpdir}}/contigs.list # Create the genomicsdb -rm -rf pon_db +rm -rf ${{tmpdir}}/pon_db gatk --java-options '-Xms10000m -Xmx20000m' GenomicsDBImport \ --tmp-dir ${{tmpdir}} \ --reference {snakemake.config[static_data_config][reference][path]} \ @@ -86,13 +87,28 @@ bgzip ${{out_base}}.vcf tabix -f ${{out_base}}.vcf.gz -pushd $tmpdir && \ - for f in ${{out_base}}.*; do \ - md5sum $f >$f.md5; \ - done && \ - popd - -mv ${{out_base}}.* $(dirname {snakemake.output.vcf}) +# Make a copy of the genomics database for PureCN +# NOTE: the sleep & true commands are required to work around +# a tar error triggered by a cephfs bug/feature +# (https://ceph-users.ceph.narkive.com/th0JxsKR/cephfs-tar-archiving-immediately-after-writing) +# The bug is probably triggered because GATK genomicsdb is large is size & can contain 100000s files +sleep 10 +tar -zcvf {snakemake.output.db} -C ${{tmpdir}} pon_db || true + +# Copy the results to destination & compute checksums +cp ${{out_base}}.vcf.gz {snakemake.output.vcf} +cp ${{out_base}}.vcf.gz.tbi {snakemake.output.vcf}.tbi + +pushd $(dirname {snakemake.output.vcf}) +f=$(basename {snakemake.output.vcf}) +md5sum $f > $f.md5 +md5sum $f.tbi > $f.tbi.md5 +popd + +pushd $(dirname {snakemake.output.db}) +f=$(basename {snakemake.output.db}) +md5sum $f > $f.md5 +popd """ ) diff --git a/snappy_wrappers/wrappers/scarHRD/gcreference/environment.yaml b/snappy_wrappers/wrappers/purecn/coverage/environment.yaml similarity index 100% rename from snappy_wrappers/wrappers/scarHRD/gcreference/environment.yaml rename to snappy_wrappers/wrappers/purecn/coverage/environment.yaml diff --git a/snappy_wrappers/wrappers/purecn/coverage/wrapper.py b/snappy_wrappers/wrappers/purecn/coverage/wrapper.py new file mode 100644 index 000000000..20ae81288 --- /dev/null +++ b/snappy_wrappers/wrappers/purecn/coverage/wrapper.py @@ -0,0 +1,100 @@ +# -*- coding: utf-8 -*- +"""CUBI+Snakemake wrapper code for computing PureCN coverage +""" + +import os + +from snakemake import shell + +__author__ = "Eric Blanc " + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step]["purecn"] + +if "container" in snakemake.input.keys() and snakemake.input.container: + container = snakemake.input.container +elif "path_container" in config.keys() and config["path_container"]: + container = config["path_container"] +else: + raise Exception("No path to PureCN container") + +if "intervals" in snakemake.input.keys() and snakemake.input.intervals: + intervals = snakemake.input.intervals +elif "path_intervals" in config.keys() and config["path_intervals"]: + intervals = config["path_intervals"] +else: + raise Exception("No path to PureCN intervals") + +# Prepare files and directories that must be accessible by the container +files_to_bind = { + "bam": snakemake.input.bam, +} +if "intervals" not in snakemake.input.keys(): + files_to_bind["intervals"] = intervals + +# Replace with full absolute paths +files_to_bind = {k: os.path.realpath(v) for k, v in files_to_bind.items()} +# Directories that mut be bound +dirs_to_bind = {k: os.path.dirname(v) for k, v in files_to_bind.items()} +# List of unique directories to bind: on cluster: -> from container: /bindings/d) +bound_dirs = {e[1]: e[0] for e in enumerate(list(set(dirs_to_bind.values())))} +# Binding command +bindings = " ".join(["-B {}:/bindings/d{}:ro".format(k, v) for k, v in bound_dirs.items()]) +# Path to files from the container +bound_files = { + k: "/bindings/d{}/{}".format(bound_dirs[dirs_to_bind[k]], os.path.basename(v)) + for k, v in files_to_bind.items() +} + +if "intervals" in bound_files.keys(): + intervals = bound_files["intervals"] + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Also pipe everything to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec &> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Setup auto-cleaned tmpdir +export tmpdir=$(mktemp -d) +trap "rm -rf $tmpdir" EXIT + +# Create coverage +cmd="/usr/local/bin/Rscript /opt/PureCN/Coverage.R --force \ + --seed {config[seed]} \ + --out-dir $(dirname {snakemake.output.coverage}) \ + --bam {bound_files[bam]} \ + --intervals {intervals} +" +mkdir -p $(dirname {snakemake.output.coverage}) +apptainer exec --home $PWD {bindings} {container} $cmd + +pushd $(dirname {snakemake.output.coverage}) +md5sum $(basename {snakemake.output.coverage}) > $(basename {snakemake.output.coverage}).md5 +popd +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/scarHRD/install/environment.yaml b/snappy_wrappers/wrappers/purecn/create_panel/environment.yaml similarity index 100% rename from snappy_wrappers/wrappers/scarHRD/install/environment.yaml rename to snappy_wrappers/wrappers/purecn/create_panel/environment.yaml diff --git a/snappy_wrappers/wrappers/purecn/create_panel/wrapper.py b/snappy_wrappers/wrappers/purecn/create_panel/wrapper.py new file mode 100644 index 000000000..9ee6f63d4 --- /dev/null +++ b/snappy_wrappers/wrappers/purecn/create_panel/wrapper.py @@ -0,0 +1,100 @@ +# -*- coding: utf-8 -*- +"""CUBI+Snakemake wrapper code for preparing PureCN panel of normals +""" + +import os +import tempfile + +from snakemake import shell + +__author__ = "Eric Blanc " + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step]["purecn"] + +if "genomicsDB" in config.keys() and config["genomicsDB"]: + genomicsDB = config["genomicsDB"] +else: + genomicsDB = "" + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Also pipe everything to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec &> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Setup auto-cleaned tmpdir +export tmpdir=$(mktemp -d) +trap "rm -rf $tmpdir" EXIT + +# MD5 checksums without dirname +md5() {{ + fn=$1 + d=$(dirname $fn) + f=$(basename $fn) + pushd $d 1> /dev/null 2>&1 + checksum=$(md5sum $f) + popd 1> /dev/null 2>&1 + echo $checksum +}} + +outdir=$tmpdir/out +mkdir -p $outdir + +mkdir $tmpdir/extra +echo "{snakemake.input.normals}" | tr " " "\n" > $tmpdir/extra/filenames.txt + +# Extract Mutect2 genomicsDB when present +if [[ -n "{genomicsDB}" ]] +then + pushd $tmpdir ; tar -zxvf {genomicsDB} ; popd + normal_panel=" --normal-panel /pon_db " +else + mkdir $tmpdir/pon_db + normal_panel="" +fi + +# Create panel +cmd="/usr/local/bin/Rscript /opt/PureCN/NormalDB.R \ + --out-dir /output \ + --coverage-files /extra/filenames.txt $normal_panel \ + --genome {config[genome_name]} --assay {config[enrichment_kit_name]} +" +apptainer exec --home $PWD -B $outdir:/output -B $tmpdir/pon_db:/pon_db:ro -B $tmpdir/extra:/extra:ro {snakemake.input.container} $cmd + +# Move output to destination +mv $outdir/normalDB_{config[enrichment_kit_name]}_{config[genome_name]}.rds {snakemake.output.db} +mv $outdir/mapping_bias_{config[enrichment_kit_name]}_{config[genome_name]}.rds {snakemake.output.mapbias} +mv $outdir/mapping_bias_hq_sites_{config[enrichment_kit_name]}_{config[genome_name]}.bed {snakemake.output.hq} +mv $outdir/low_coverage_targets_{config[enrichment_kit_name]}_{config[genome_name]}.bed {snakemake.output.lowcov} +mv $outdir/interval_weights_{config[enrichment_kit_name]}_{config[genome_name]}.png {snakemake.output.plot} + +# MD5 checksum for main result only +md5 {snakemake.output.db} > {snakemake.output.db}.md5 +md5 {snakemake.output.mapbias} > {snakemake.output.mapbias}.md5 +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/purecn/environment.yaml b/snappy_wrappers/wrappers/purecn/environment.yaml new file mode 100644 index 000000000..514a8220e --- /dev/null +++ b/snappy_wrappers/wrappers/purecn/environment.yaml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - htslib diff --git a/snappy_wrappers/wrappers/purecn/prepare/environment.yaml b/snappy_wrappers/wrappers/purecn/prepare/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/purecn/prepare/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/purecn/prepare/wrapper.py b/snappy_wrappers/wrappers/purecn/prepare/wrapper.py new file mode 100644 index 000000000..f72addccc --- /dev/null +++ b/snappy_wrappers/wrappers/purecn/prepare/wrapper.py @@ -0,0 +1,108 @@ +# -*- coding: utf-8 -*- +"""CUBI+Snakemake wrapper code for preparing exome kit intervals for PureCN +""" + +import os + +from snakemake import shell + +__author__ = "Eric Blanc " + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step]["purecn"] + +genome = snakemake.config["static_data_config"]["reference"]["path"] + +# Prepare files and directories that must be accessible by the container +bound_files = { + "genome": os.path.normpath(genome), + "path_bait_regions": os.path.normpath(config["path_bait_regions"]), + "mappability": os.path.normpath(config["mappability"]) + if "mappability" in config and config["mappability"] + else "", + "reptiming": os.path.normpath(config["reptiming"]) + if "reptiming" in config and config["reptiming"] + else "", +} + +keys = list(bound_files.keys()) +bindings = [] +for i in range(len(keys)): + k = keys[i] + if bound_files[k]: + # Binding directory to /bindings/d + bindings.append(" -B {}:/bindings/d{}:ro".format(os.path.dirname(bound_files[k]), i)) + bound_files[k] = "/bindings/d{}/{}".format(i, os.path.basename(bound_files[k])) +bindings = " ".join(bindings) + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Also pipe everything to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec &> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Setup auto-cleaned tmpdir +export tmpdir=$(mktemp -d) +trap "rm -rf $tmpdir" EXIT + +md5() {{ + d=$(dirname $1) + f=$(basename $1) + pushd $d 1> /dev/null 2>&1 + md5sum $f > $f.md5 + popd 1> /dev/null 2>&1 +}} + +# Create panel +uncompressed=$(echo "{snakemake.output.optimized}" | sed -e "s/\.gz$//") + +cmd="/usr/local/bin/Rscript /opt/PureCN/IntervalFile.R \ + --out-file {snakemake.output.intervals} \ + --export $uncompressed \ + --in-file {bound_files[path_bait_regions]} \ + --fasta {bound_files[genome]} --genome {config[genome_name]} \ + $(if [[ -n "{bound_files[mappability]}" ]]; then \ + echo "--mappability {bound_files[mappability]}" + fi) \ + $(if [[ -n "{bound_files[reptiming]}" ]]; then \ + echo "--reptiming {bound_files[reptiming]}" + fi) +" + +mkdir -p $(dirname {snakemake.output.intervals}) +mkdir -p $(dirname $uncompressed) + +apptainer exec --home $PWD {bindings} {snakemake.input.container} $cmd + +bgzip $uncompressed +tabix {snakemake.output.optimized} + +md5 {snakemake.output.intervals} +md5 {snakemake.output.optimized} +md5 {snakemake.output.optimized}.tbi +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/purecn/run/environment.yaml b/snappy_wrappers/wrappers/purecn/run/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/purecn/run/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/purecn/run/wrapper.py b/snappy_wrappers/wrappers/purecn/run/wrapper.py new file mode 100644 index 000000000..0db05d037 --- /dev/null +++ b/snappy_wrappers/wrappers/purecn/run/wrapper.py @@ -0,0 +1,128 @@ +# -*- coding: utf-8 -*- +"""CUBI+Snakemake wrapper code for computing CNV using PureCN +""" + +import os + +from snakemake import shell + +__author__ = "Eric Blanc " + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step]["purecn"] + +# WARNING- these extra commands cannot contain file paths +extra_commands = " ".join( + [ + " --{}={}".format(k, v) if v else " --{}".format(k) + for k, v in config["extra_commands"].items() + ] +) + +# List files that must be accessible from the container +files_to_bind = { + "vcf": snakemake.input.vcf, + "mapping_bias": config["path_mapping_bias"], + "normaldb": config["path_panel_of_normals"], + "intervals": config["path_intervals"], +} +if "snp_blacklist" in config.keys() and config["snp_blacklist"]: + files_to_bind["snp-blacklist"] = config["snp_blacklist"] +if "segments" in snakemake.input.keys() and snakemake.input.segments: + files_to_bind["seg-file"] = snakemake.input.segments +if "log2" in snakemake.input.keys() and snakemake.input.log2: + files_to_bind["log-ratio-file"] = snakemake.input.log2 + +# TODO: Put the following in a function (decide where...) +# Replace with full absolute paths +files_to_bind = {k: os.path.realpath(v) for k, v in files_to_bind.items()} +# Directories that mut be bound +dirs_to_bind = {k: os.path.dirname(v) for k, v in files_to_bind.items()} +# List of unique directories to bind: on cluster: -> from container: /bindings/d) +bound_dirs = {e[1]: e[0] for e in enumerate(list(set(dirs_to_bind.values())))} +# Binding command +bindings = " ".join(["-B {}:/bindings/d{}:ro".format(k, v) for k, v in bound_dirs.items()]) +# Path to files from the container +bound_files = { + k: "/bindings/d{}/{}".format(bound_dirs[dirs_to_bind[k]], os.path.basename(v)) + for k, v in files_to_bind.items() +} + +if "snp-blacklist" in bound_files.keys(): + extra_commands += " --snp-blacklist={}".format(bound_files["snp-blacklist"]) +if "seg-file" in bound_files.keys(): + extra_commands += " --seg-file={}".format(bound_files["seg-file"]) +if "log-ratio-file" in bound_files.keys(): + extra_commands += " --log-ratio-file={}".format(bound_files["log-ratio-file"]) + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Also pipe everything to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec &> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Setup auto-cleaned tmpdir +export tmpdir=$(mktemp -d) +trap "rm -rf $tmpdir" EXIT + +# Compute md5 checksum +md5() {{ + fn=$1 + d=$(dirname $fn) + f=$(basename $fn) + pushd $d 1> /dev/null 2>&1 + checksum=$(md5sum $f) + popd 1> /dev/null 2>&1 + echo "$checksum" +}} + +outdir=$(dirname {snakemake.output.segments}) +mkdir -p $outdir + +# Run PureCN with a panel of normals +cmd="/usr/local/bin/Rscript PureCN.R \ + --sampleid {snakemake.wildcards[library_name]} \ + --tumor {snakemake.input.tumor} \ + --vcf {bound_files[vcf]} \ + --mapping-bias-file {bound_files[mapping_bias]} \ + --normaldb {bound_files[normaldb]} \ + --intervals {bound_files[intervals]} \ + --genome {config[genome_name]} \ + --out $outdir --out-vcf --force \ + --seed {config[seed]} --parallel --cores={snakemake.threads} \ + {extra_commands} +" +apptainer exec --home $PWD {bindings} {config[path_container]} $cmd + +md5 {snakemake.output.segments} > {snakemake.output.segments_md5} +md5 {snakemake.output.ploidy} > {snakemake.output.ploidy_md5} +md5 {snakemake.output.pvalues} > {snakemake.output.pvalues_md5} +md5 {snakemake.output.vcf} > {snakemake.output.vcf_md5} +md5 {snakemake.output.vcf_tbi} > {snakemake.output.vcf_tbi_md5} +md5 {snakemake.output.loh} > {snakemake.output.loh_md5} +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/r/environment.yaml b/snappy_wrappers/wrappers/r/environment.yaml new file mode 100644 index 000000000..20218ccdf --- /dev/null +++ b/snappy_wrappers/wrappers/r/environment.yaml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - r-base + - r-remotes + - r-biocmanager \ No newline at end of file diff --git a/snappy_wrappers/wrappers/r/wrapper.py b/snappy_wrappers/wrappers/r/wrapper.py new file mode 100644 index 000000000..059419c33 --- /dev/null +++ b/snappy_wrappers/wrappers/r/wrapper.py @@ -0,0 +1,69 @@ +"""CUBI+Snakemake wrapper code for non-conda package installation +""" + +from snakemake import shell + +__author__ = "Eric Blanc " + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step] + +if "packages" in snakemake.params.keys(): + packages = snakemake.params["packages"] +elif "packages" in config.keys(): + packages = config["packages"] +else: + packages = None + +assert packages is not None +assert isinstance(packages, list) +assert len(packages) > 0 + +to_install = [] +for package in packages: + package = dict(package) + to_install.append('list(name="{}", repo="{}")'.format(package["name"], package["repo"])) +to_install = "list({})".format(", ".join(to_install)) + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Also pipe stderr to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +R --vanilla --slave << __EOF +for (pkg in {to_install}) {{ + if (pkg[["repo"]] == "cran") install.packages(pkg[["name"]], lib=dirname("{snakemake.output.done}"), update=FALSE, ask=FALSE) + if (pkg[["repo"]] == "bioconductor") BiocManager::install(pkg[["name"]], lib=dirname("{snakemake.output.done}"), update=FALSE, ask=FALSE) + if (pkg[["repo"]] == "github") remotes::install_github(pkg[["name"]], lib=dirname("{snakemake.output.done}"), upgrade="never") + if (pkg[["repo"]] == "bitbucket") remotes::install_bitbucket(pkg[["name"]], lib=dirname("{snakemake.output.done}"), upgrade="never") + if (pkg[["repo"]] == "local") remotes::install_local(pkg[["name"]], lib=dirname("{snakemake.output.done}"), upgrade="never") +}} +__EOF +touch {snakemake.output.done} +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/scarHRD/environment.yaml b/snappy_wrappers/wrappers/scarHRD/environment.yaml index b6a8c8b49..a86405d52 100644 --- a/snappy_wrappers/wrappers/scarHRD/environment.yaml +++ b/snappy_wrappers/wrappers/scarHRD/environment.yaml @@ -3,8 +3,4 @@ channels: - bioconda dependencies: - python =3.9 - - sequenza-utils - - r-sequenza - - r-devtools - - r-data.table - - samtools + - r-base diff --git a/snappy_wrappers/wrappers/scarHRD/run/wrapper.py b/snappy_wrappers/wrappers/scarHRD/run/wrapper.py index 6e414eade..7e1261fa5 100644 --- a/snappy_wrappers/wrappers/scarHRD/run/wrapper.py +++ b/snappy_wrappers/wrappers/scarHRD/run/wrapper.py @@ -7,7 +7,7 @@ __author__ = "Eric Blanc " -lib_path = os.path.dirname(snakemake.input.lib_path) +lib_path = os.path.dirname(snakemake.input.done) step = snakemake.config["pipeline_step"]["name"] genome = snakemake.config["static_data_config"]["reference"]["path"] @@ -46,19 +46,16 @@ fi fi -sequenza-utils bam2seqz \ - -gc {snakemake.input.gc} --fasta {genome} \ - -n {snakemake.input.normal_bam} --tumor {snakemake.input.tumor_bam} \ - -C {chromosomes} \ - | sequenza-utils seqz_binning -w {length} -s - \ - | gzip > {snakemake.output.sequenza} +export R_LIBS_USER="{lib_path}" +export VROOM_CONNECTION_SIZE=2000000000 + +export R_LIBS_PATH="{lib_path}" +export VROOM_CONNECTION_SIZE=2000000000 cat << __EOF | R --vanilla --slave -.libPaths(c("{lib_path}", .libPaths())) -Sys.setenv(VROOM_CONNECTION_SIZE=2000000000) library("scarHRD") -tbl <- scar_score("{snakemake.output.sequenza}", reference="{genome_name}", seqz=TRUE, chr.in.name={chr_in_name}) +tbl <- scar_score("{snakemake.input.seqz}", reference="{genome_name}", seqz=TRUE, chr.in.name={chr_in_name}, outputdir=dirname("{snakemake.output.scarHRD}")) cat('{{\n', file="{snakemake.output.scarHRD}") cat(' "HRD": ', tbl[1,1], ',\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) cat(' "Telomeric AI": ', tbl[1,2], ',\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) @@ -68,7 +65,6 @@ __EOF -pushd $(dirname {snakemake.output.sequenza}) ; f=$(basename {snakemake.output.sequenza}) ; md5sum $f > $f.md5 ; popd pushd $(dirname {snakemake.output.scarHRD}) ; f=$(basename {snakemake.output.scarHRD}) ; md5sum $f > $f.md5 ; popd """ ) diff --git a/snappy_wrappers/wrappers/sequenza/environment.yaml b/snappy_wrappers/wrappers/sequenza/environment.yaml new file mode 100644 index 000000000..b6a8c8b49 --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/environment.yaml @@ -0,0 +1,10 @@ +channels: + - conda-forge + - bioconda +dependencies: + - python =3.9 + - sequenza-utils + - r-sequenza + - r-devtools + - r-data.table + - samtools diff --git a/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml b/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/scarHRD/gcreference/wrapper.py b/snappy_wrappers/wrappers/sequenza/gcreference/wrapper.py similarity index 80% rename from snappy_wrappers/wrappers/scarHRD/gcreference/wrapper.py rename to snappy_wrappers/wrappers/sequenza/gcreference/wrapper.py index 1b9a2c4b0..0b230a26d 100644 --- a/snappy_wrappers/wrappers/scarHRD/gcreference/wrapper.py +++ b/snappy_wrappers/wrappers/sequenza/gcreference/wrapper.py @@ -1,4 +1,4 @@ -"""CUBI+Snakemake wrapper code for scarHRD (sequenza GC reference file) +"""CUBI+Snakemake wrapper code for sequenza GC reference file """ import os @@ -9,7 +9,7 @@ step = snakemake.config["pipeline_step"]["name"] genome = snakemake.config["static_data_config"]["reference"]["path"] -length = snakemake.config["step_config"][step]["scarHRD"]["length"] +length = snakemake.config["step_config"][step]["sequenza"]["length"] shell.executable("/bin/bash") @@ -34,10 +34,11 @@ fi fi -sequenza-utils gc_wiggle --fasta {genome} -w {length} -o {snakemake.output} +sequenza-utils gc_wiggle --fasta {genome} -w {length} -o {snakemake.output.gc} -pushd $(dirname {snakemake.output}) -md5sum $(basename {snakemake.output}) > $(basename {snakemake.output}).md5 +pushd $(dirname {snakemake.output.gc}) +md5sum $(basename {snakemake.output.gc}) > $(basename {snakemake.output.gc}).md5 +popd """ ) diff --git a/snappy_wrappers/wrappers/sequenza/report/environment.yaml b/snappy_wrappers/wrappers/sequenza/report/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/report/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/sequenza/report/wrapper.py b/snappy_wrappers/wrappers/sequenza/report/wrapper.py new file mode 100644 index 000000000..28c1b18a6 --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/report/wrapper.py @@ -0,0 +1,98 @@ +"""CUBI+Snakemake wrapper code for sequenza (R part, post-processing) +""" + +import os +import sys + +# The following is required for being able to import snappy_wrappers modules +# inside wrappers. These run in an "inner" snakemake process which uses its +# own conda environment which cannot see the snappy_pipeline installation. +base_dir = os.path.normpath(os.path.join(os.path.dirname(__file__), "..", "..", "..", "..")) +sys.path.insert(0, base_dir) + +from snakemake import shell + +from snappy_wrappers.tools.genome_windows import yield_contigs + +__author__ = "Eric Blanc " + + +def config_to_r(x): + if x is None: + return "NULL" + if isinstance(x, str): + return f'"{x}"' + if isinstance(x, bool): + return "TRUE" if x else "FALSE" + if isinstance(x, list): + return "c({})".format(", ".join([config_to_r(xx) for xx in x])) + if isinstance(x, dict): + return "list({})".format( + ", ".join(['"{}"={}'.format(k, config_to_r(v)) for k, v in x.items()]) + ) + return str(x) + + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step]["sequenza"] +genome = snakemake.config["static_data_config"]["reference"]["path"] + +f = open(genome + ".fai", "rt") +contigs = config_to_r(list(yield_contigs(f, config.get("ignore_chroms")))) +f.close() + +args_extract = config_to_r(dict(config["extra_args_extract"])) +args_fit = config_to_r(dict(config["extra_args_fit"])) + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Also pipe stderr to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +export R_LIBS_USER=$(dirname {snakemake.input.packages}) + +R --vanilla --slave << __EOF +library(sequenza) + +args <- list(file="{snakemake.input.seqz}", assembly="{config[assembly]}", chromosome.list={contigs}) +args <- c(args, {args_extract}) +seqz <- do.call(sequenza.extract, args=args) + +args <- list(sequenza.extract=seqz, chromosome.list={contigs}, mc.cores=1) +args <- c(args, {args_fit}) +CP <- do.call(sequenza.fit, args=args) + +sequenza.results(sequenza.extract=seqz, cp.table=CP, sample.id="{snakemake.params[sample_id]}", out.dir=dirname("{snakemake.output.done}")) + +__EOF + +pushd $(dirname {snakemake.output.done}) ; for f in $(ls) ; do md5sum $f > $f.md5 ; done ; popd + +touch {snakemake.output.done} +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/sequenza/run/environment.yaml b/snappy_wrappers/wrappers/sequenza/run/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/run/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/sequenza/run/wrapper.py b/snappy_wrappers/wrappers/sequenza/run/wrapper.py new file mode 100644 index 000000000..13fa1f64d --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/run/wrapper.py @@ -0,0 +1,71 @@ +"""CUBI+Snakemake wrapper code for sequenza (sequenza-utils, pileups) +""" + +import os +import sys + +# The following is required for being able to import snappy_wrappers modules +# inside wrappers. These run in an "inner" snakemake process which uses its +# own conda environment which cannot see the snappy_pipeline installation. +base_dir = os.path.normpath(os.path.join(os.path.dirname(__file__), "..", "..", "..", "..")) +sys.path.insert(0, base_dir) + +from snakemake import shell + +from snappy_wrappers.tools.genome_windows import yield_contigs + +__author__ = "Eric Blanc " + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step]["sequenza"] +genome = snakemake.config["static_data_config"]["reference"]["path"] +length = config["length"] + +f = open(genome + ".fai", "rt") +contigs = " ".join(yield_contigs(f, config.get("ignore_chroms"))) +f.close() + +extra_arguments = " ".join( + ["--{} {}".format(k, v) for k, v in config.get("extra_arguments", {}).items()] +) + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Also pipe stderr to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +sequenza-utils bam2seqz \ + -gc {snakemake.input.gc} --fasta {genome} \ + -n {snakemake.input.normal_bam} --tumor {snakemake.input.tumor_bam} \ + -C {contigs} {extra_arguments} \ + | sequenza-utils seqz_binning -s - \ + -w {length} -o {snakemake.output.seqz} + +pushd $(dirname {snakemake.output.seqz}) ; f=$(basename {snakemake.output.seqz}) ; md5sum $f > $f.md5 ; popd +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/singularity/environment.yaml b/snappy_wrappers/wrappers/singularity/environment.yaml new file mode 100644 index 000000000..894ebc8c5 --- /dev/null +++ b/snappy_wrappers/wrappers/singularity/environment.yaml @@ -0,0 +1,2 @@ +dependencies: + - python diff --git a/snappy_wrappers/wrappers/scarHRD/install/wrapper.py b/snappy_wrappers/wrappers/singularity/wrapper.py similarity index 56% rename from snappy_wrappers/wrappers/scarHRD/install/wrapper.py rename to snappy_wrappers/wrappers/singularity/wrapper.py index a9a9c15e0..f04eebdcc 100644 --- a/snappy_wrappers/wrappers/scarHRD/install/wrapper.py +++ b/snappy_wrappers/wrappers/singularity/wrapper.py @@ -1,13 +1,20 @@ -"""CUBI+Snakemake wrapper code for scarHRD (non-conda package installation) +# -*- coding: utf-8 -*- +"""CUBI+Snakemake wrapper code for preparing exome kit intervals for PureCN """ -import os - from snakemake import shell __author__ = "Eric Blanc " -lib_path = os.path.dirname(snakemake.output.lib_path) +container = None +if "container" in snakemake.params.keys() and snakemake.params["container"]: + container = snakemake.params["container"] +else: + step = snakemake.config["pipeline_step"]["name"] + config = snakemake.config["step_config"][step] + if "container" in config.keys() and config["container"]: + container = config["container"] +assert container, "Missing or illegal container image address" shell.executable("/bin/bash") @@ -15,28 +22,24 @@ r""" set -x -# Write out information about conda installation. -conda list >{snakemake.log.conda_list} -conda info >{snakemake.log.conda_info} -md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} -md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} - -# Also pipe stderr to log file +# Also pipe everything to log file if [[ -n "{snakemake.log.log}" ]]; then if [[ "$(set +e; tty; set -e)" != "" ]]; then rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) - exec 2> >(tee -a "{snakemake.log.log}" >&2) + exec &> >(tee -a "{snakemake.log.log}" >&2) else rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) echo "No tty, logging disabled" >"{snakemake.log.log}" fi fi -R --vanilla --slave << __EOF -devtools::install_github("aroneklund/copynumber", lib="{lib_path}", upgrade="never") -devtools::install_github("sztup/scarHRD", lib="{lib_path}", upgrade="never") -__EOF -touch {snakemake.output} +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +apptainer pull --name {snakemake.output.container} {container} """ ) diff --git a/tests/snappy_pipeline/workflows/test_workflows_homologous_recombination_deficiency.py b/tests/snappy_pipeline/workflows/test_workflows_homologous_recombination_deficiency.py index 3183a63e7..4ec289fd5 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_homologous_recombination_deficiency.py +++ b/tests/snappy_pipeline/workflows/test_workflows_homologous_recombination_deficiency.py @@ -31,12 +31,12 @@ def minimal_config(): step_config: ngs_mapping: tools: - dna: ['bwa'] - bwa: - path_index: /path/to/bwa/index.fasta + dna: [bwa] + somatic_targeted_seq_cnv_calling: + tools: ['sequenza'] homologous_recombination_deficiency: tools: ['scarHRD'] - path_ngs_mapping: ../ngs_mapping # REQUIRED + path_cnv_calling: ../somatic_targeted_seq_cnv_calling # REQUIRED data_sets: first_batch: @@ -64,7 +64,7 @@ def homologous_recombination_deficiency_workflow( """Return HomologousRecombinationDeficiencyWorkflow object pre-configured with cancer sheet""" # Patch out file-system related things in abstract (the crawling link in step is defined there) patch_module_fs("snappy_pipeline.workflows.abstract", cancer_sheet_fake_fs, mocker) - dummy_workflow.globals = {"ngs_mapping": lambda x: "NGS_MAPPING/" + x} + dummy_workflow.globals = {"cnv_calling": lambda x: "SOMATIC_CNV_CALLING/" + x} # Construct the workflow object return HomologousRecombinationDeficiencyWorkflow( dummy_workflow, @@ -80,14 +80,12 @@ def homologous_recombination_deficiency_workflow( def test_scarHRD_step_part_get_input_files_run(homologous_recombination_deficiency_workflow): """Tests ScarHRDStepPart.get_input_files() - run""" - wildcards = Wildcards(fromdict={"library_name": "P001-T1-DNA1-WGS1", "mapper": "bwa"}) + wildcards = Wildcards( + fromdict={"mapper": "bwa", "caller": "sequenza", "library_name": "P001-T1-DNA1-WGS1"} + ) expected = { - "lib_path": "work/R_packages/out/.done", - "gc": "work/static_data/out/grch37_50.wig.gz", - "normal_bai": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam.bai", - "normal_bam": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam", - "tumor_bai": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam.bai", - "tumor_bam": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam", + "done": "work/R_packages/out/scarHRD.done", + "seqz": "SOMATIC_CNV_CALLING/output/bwa.sequenza.P001-T1-DNA1-WGS1/out/bwa.sequenza.P001-T1-DNA1-WGS1.seqz.gz", } actual = homologous_recombination_deficiency_workflow.get_input_files("scarHRD", "run")( wildcards @@ -98,10 +96,12 @@ def test_scarHRD_step_part_get_input_files_run(homologous_recombination_deficien def test_scarHRD_step_part_get_output_files_run(homologous_recombination_deficiency_workflow): """Tests ScarHRDStepPart.get_output_files() - run""" # Define expected - base_name_out = "work/{mapper}.scarHRD.{library_name}/out/{mapper}.scarHRD.{library_name}" + base_name_out = ( + "work/{mapper}.{caller}.scarHRD.{library_name}/out/{mapper}.{caller}.scarHRD.{library_name}" + ) expected = { - "sequenza": base_name_out + ".seqz.gz", "scarHRD": base_name_out + ".json", + "scarHRD_md5": base_name_out + ".json.md5", } # Get actual actual = homologous_recombination_deficiency_workflow.get_output_files("scarHRD", "run") @@ -110,7 +110,9 @@ def test_scarHRD_step_part_get_output_files_run(homologous_recombination_deficie def test_scarHRD_step_part_get_log_file_run(homologous_recombination_deficiency_workflow): """Tests ScarHRDStepPart.get_log_file() - run""" - base_name = "work/{mapper}.scarHRD.{library_name}/log/{mapper}.scarHRD.{library_name}" + base_name = ( + "work/{mapper}.{caller}.scarHRD.{library_name}/log/{mapper}.{caller}.scarHRD.{library_name}" + ) expected = get_expected_log_files_dict(base_out=base_name) actual = homologous_recombination_deficiency_workflow.get_log_file("scarHRD", "run") assert actual == expected @@ -119,7 +121,7 @@ def test_scarHRD_step_part_get_log_file_run(homologous_recombination_deficiency_ def test_scarHRD_step_part_get_resource_usage_run(homologous_recombination_deficiency_workflow): """Tests ScarHRDStepPart.get_resource() - run""" # Define expected - expected_dict = {"threads": 2, "time": "48:00:00", "memory": "32G", "partition": "medium"} + expected_dict = {"threads": 1, "time": "24:00:00", "memory": "32G", "partition": "medium"} # Evaluate for resource, expected in expected_dict.items(): msg_error = f"Assertion error for resource '{resource}'." @@ -132,7 +134,7 @@ def test_scarHRD_step_part_get_resource_usage_run(homologous_recombination_defic def test_scarHRD_step_part_get_output_files_install(homologous_recombination_deficiency_workflow): """Tests ScarHRDStepPart.get_output_files() - install""" # Define expected - expected = {"lib_path": "work/R_packages/out/.done"} + expected = {"done": "work/R_packages/out/scarHRD.done"} # Get actual actual = homologous_recombination_deficiency_workflow.get_output_files("scarHRD", "install") assert actual == expected @@ -140,7 +142,7 @@ def test_scarHRD_step_part_get_output_files_install(homologous_recombination_def def test_scarHRD_step_part_get_log_file_install(homologous_recombination_deficiency_workflow): """Tests ScarHRDStepPart.get_log_file() - install""" - base_name = "work/R_packages/log/R_packages" + base_name = "work/R_packages/log/scarHRD" expected = get_expected_log_files_dict(base_out=base_name) actual = homologous_recombination_deficiency_workflow.get_log_file("scarHRD", "install") assert actual == expected @@ -149,7 +151,7 @@ def test_scarHRD_step_part_get_log_file_install(homologous_recombination_deficie def test_scarHRD_step_part_get_resource_usage_install(homologous_recombination_deficiency_workflow): """Tests ScarHRDStepPart.get_resource() - install""" # Define expected - expected_dict = {"threads": 1, "time": "02:00:00", "memory": "4096M", "partition": "short"} + expected_dict = {"threads": 1, "time": "01:00:00", "memory": "2G", "partition": "medium"} # Evaluate for resource, expected in expected_dict.items(): msg_error = f"Assertion error for resource '{resource}'." @@ -159,25 +161,6 @@ def test_scarHRD_step_part_get_resource_usage_install(homologous_recombination_d assert actual == expected, msg_error -def test_scarHRD_step_part_get_output_files_gcreference( - homologous_recombination_deficiency_workflow, -): - """Tests ScarHRDStepPart.get_output_files() - gcreference""" - # Define expected - expected = {"gc": "work/static_data/out/grch37_50.wig.gz"} - # Get actual - actual = homologous_recombination_deficiency_workflow.get_output_files("scarHRD", "gcreference") - assert actual == expected - - -def test_scarHRD_step_part_get_log_file_gcreference(homologous_recombination_deficiency_workflow): - """Tests ScarHRDStepPart.get_log_file() - gcreference""" - base_name = "work/static_data/log/grch37_50" - expected = get_expected_log_files_dict(base_out=base_name) - actual = homologous_recombination_deficiency_workflow.get_log_file("scarHRD", "gcreference") - assert actual == expected - - # Tests for SomaticMsiCallingWorkflow -------------------------------------------------------------- @@ -188,12 +171,18 @@ def test_homologous_recombination_deficiency_workflow(homologous_recombination_d assert list(sorted(homologous_recombination_deficiency_workflow.sub_steps.keys())) == expected # Check result file construction expected = [ - "output/bwa.scarHRD.P001-T1-DNA1-WGS1/out/bwa.scarHRD.P001-T1-DNA1-WGS1.json", - "output/bwa.scarHRD.P001-T1-DNA1-WGS1/out/bwa.scarHRD.P001-T1-DNA1-WGS1.seqz.gz", - "output/bwa.scarHRD.P002-T1-DNA1-WGS1/out/bwa.scarHRD.P002-T1-DNA1-WGS1.json", - "output/bwa.scarHRD.P002-T1-DNA1-WGS1/out/bwa.scarHRD.P002-T1-DNA1-WGS1.seqz.gz", - "output/bwa.scarHRD.P002-T2-DNA1-WGS1/out/bwa.scarHRD.P002-T2-DNA1-WGS1.json", - "output/bwa.scarHRD.P002-T2-DNA1-WGS1/out/bwa.scarHRD.P002-T2-DNA1-WGS1.seqz.gz", + "output/bwa.sequenza.scarHRD.P001-T1-DNA1-WGS1/out/bwa.sequenza.scarHRD.P001-T1-DNA1-WGS1.json", + "output/bwa.sequenza.scarHRD.P002-T1-DNA1-WGS1/out/bwa.sequenza.scarHRD.P002-T1-DNA1-WGS1.json", + "output/bwa.sequenza.scarHRD.P002-T2-DNA1-WGS1/out/bwa.sequenza.scarHRD.P002-T2-DNA1-WGS1.json", + "output/bwa.sequenza.scarHRD.P001-T1-DNA1-WGS1/out/bwa.sequenza.scarHRD.P001-T1-DNA1-WGS1.json.md5", + "output/bwa.sequenza.scarHRD.P002-T1-DNA1-WGS1/out/bwa.sequenza.scarHRD.P002-T1-DNA1-WGS1.json.md5", + "output/bwa.sequenza.scarHRD.P002-T2-DNA1-WGS1/out/bwa.sequenza.scarHRD.P002-T2-DNA1-WGS1.json.md5", + ] + expected += [ + f"output/bwa.sequenza.scarHRD.P00{i[0]}-T{i[1]}-DNA1-WGS1/log/bwa.sequenza.scarHRD.P00{i[0]}-T{i[1]}-DNA1-WGS1.{ext}{chksum}" + for i in ((1, 1), (2, 1), (2, 2)) + for ext in ("log", "conda_list.txt", "conda_info.txt") + for chksum in ("", ".md5") ] actual = set(homologous_recombination_deficiency_workflow.get_result_files()) expected = set(expected) diff --git a/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals.py b/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals.py index 4e85cfdc1..7ac498f81 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals.py +++ b/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals.py @@ -1,6 +1,7 @@ # -*- coding: utf-8 -*- """Tests for the panel_of_normals workflow module code""" +from collections import OrderedDict import textwrap import pytest @@ -38,14 +39,18 @@ def minimal_config(): path_index: /path/to/bwa/index.fa panel_of_normals: - tools: ['mutect2', 'cnvkit', 'access'] + tools: ['mutect2', 'cnvkit', 'access', 'purecn'] + path_ngs_mapping: ../ngs_mapping mutect2: germline_resource: /path/to/germline_resource.vcf path_normals_list: "" cnvkit: path_excluded_regions: "" - path_target_regions: /path/to/regions.bed # WGS mode + path_target_regions: /path/to/regions.bed # WES mode path_normals_list: "" + purecn: + path_normals_list: "" + path_bait_regions: /path/to/baits/regions.bed data_sets: first_batch: @@ -138,6 +143,9 @@ def test_mutect2_step_part_get_output_files_create_panel(panel_of_normals_workfl """Tests Mutect2StepPart._get_output_files_create_panel()""" base_name_out = "work/{mapper}.mutect2/out/{mapper}.mutect2.panel_of_normals" expected = get_expected_output_vcf_files_dict(base_out=base_name_out) + base_name_out = "work/{mapper}.mutect2/out/{mapper}.mutect2.genomicsDB" + expected["db"] = base_name_out + ".tar.gz" + expected["db_md5"] = expected["db"] + ".md5" actual = panel_of_normals_workflow.get_output_files("mutect2", "create_panel") assert actual == expected @@ -474,13 +482,144 @@ def test_access_step_part_get_resource_usage(panel_of_normals_workflow): assert actual == expected, msg_error +# Tests for PureCnStepPart ------------------------------------------------------------------------- + + +def test_purecn_step_part_get_output_files_install(panel_of_normals_workflow): + """Tests PureCnStepPart._get_output_files_install()""" + expected = {"container": "work/containers/out/purecn.simg"} + actual = panel_of_normals_workflow.get_output_files("purecn", "install") + assert actual == expected + + +def test_purecn_step_part_get_log_file_install(panel_of_normals_workflow): + """Tests PureCnStepPart._get_log_file_install()""" + expected = get_expected_log_files_dict(base_out="work/containers/log/purecn") + actual = panel_of_normals_workflow.get_log_file("purecn", "install") + assert actual == expected + + +def test_purecn_step_part_get_input_files_prepare(panel_of_normals_workflow): + """Tests PureCnStepPart._get_input_files_prepare()""" + expected = {"container": "work/containers/out/purecn.simg"} + actual = panel_of_normals_workflow.get_input_files("purecn", "prepare") + assert actual == expected + + +def test_purecn_step_part_get_output_files_prepare(panel_of_normals_workflow): + """Tests PureCnStepPart._get_output_files_prepare()""" + expected = { + "intervals": "work/purecn/out/unknown_unknown.list", + "optimized": "work/purecn/out/unknown_unknown.bed.gz", + "tbi": "work/purecn/out/unknown_unknown.bed.gz.tbi", + "intervals_md5": "work/purecn/out/unknown_unknown.list.md5", + "optimized_md5": "work/purecn/out/unknown_unknown.bed.gz.md5", + "tbi_md5": "work/purecn/out/unknown_unknown.bed.gz.tbi.md5", + } + actual = panel_of_normals_workflow.get_output_files("purecn", "prepare") + assert actual == expected + + +def test_purecn_step_part_get_log_file_prepare(panel_of_normals_workflow): + """Tests PureCnStepPart._get_log_file_prepare()""" + expected = get_expected_log_files_dict(base_out="work/purecn/log/unknown_unknown") + actual = panel_of_normals_workflow.get_log_file("purecn", "prepare") + assert actual == expected + + +def test_purecn_step_part_get_input_files_coverage(panel_of_normals_workflow): + """Tests PureCnStepPart._get_input_files_coverage()""" + wildcards = Wildcards( + fromdict={ + "mapper": "bwa", + "normal_library": "P001-N1-DNA1-WGS1", + } + ) + expected = { + "container": "work/containers/out/purecn.simg", + "intervals": "work/purecn/out/unknown_unknown.list", + "bam": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam", + } + actual = panel_of_normals_workflow.get_input_files("purecn", "coverage")(wildcards) + assert actual == expected + + +def test_purecn_step_part_get_output_files_coverage(panel_of_normals_workflow): + """Tests PureCnStepPart._get_output_files_coverage()""" + expected = { + "coverage": "work/{mapper}.purecn/out/{mapper}.{normal_library,.+-DNA[0-9]+-WES[0-9]+}_coverage_loess.txt.gz" + } + actual = panel_of_normals_workflow.get_output_files("purecn", "coverage") + assert actual == expected + + +def test_purecn_step_part_get_log_file_coverage(panel_of_normals_workflow): + """Tests PureCnStepPart._get_log_file_coverage()""" + expected = get_expected_log_files_dict( + base_out="work/{mapper}.purecn/log/{mapper}.{normal_library,.+-DNA[0-9]+-WES[0-9]+}" + ) + actual = panel_of_normals_workflow.get_log_file("purecn", "coverage") + assert actual == expected + + +def test_purecn_step_part_get_input_files_create_panel(panel_of_normals_workflow): + """Tests PureCnStepPart._get_input_files_create_panel()""" + wildcards = Wildcards(fromdict={"mapper": "bwa"}) + expected = { + "normals": [ + "work/bwa.purecn/out/bwa.P001-N1-DNA1-WGS1_coverage_loess.txt.gz", + "work/bwa.purecn/out/bwa.P002-N1-DNA1-WGS1_coverage_loess.txt.gz", + ], + "container": "work/containers/out/purecn.simg", + } + actual = panel_of_normals_workflow.get_input_files("purecn", "create_panel")(wildcards) + assert actual == expected + + +def test_purecn_step_part_get_output_files_create_panel(panel_of_normals_workflow): + """Tests PureCnStepPart._get_output_files_create_panel()""" + expected = { + "db": "work/{mapper}.purecn/out/{mapper}.purecn.panel_of_normals.rds", + "db_md5": "work/{mapper}.purecn/out/{mapper}.purecn.panel_of_normals.rds.md5", + "mapbias": "work/{mapper}.purecn/out/{mapper}.purecn.mapping_bias.rds", + "mapbias_md5": "work/{mapper}.purecn/out/{mapper}.purecn.mapping_bias.rds.md5", + "lowcov": "work/{mapper}.purecn/out/{mapper}.purecn.low_coverage_targets.bed", + "hq": "work/{mapper}.purecn/out/{mapper}.purecn.hq_sites.bed", + "plot": "work/{mapper}.purecn/out/{mapper}.purecn.interval_weights.png", + } + actual = panel_of_normals_workflow.get_output_files("purecn", "create_panel") + assert actual == expected + + +def test_purecn_step_part_get_log_file_create_panel(panel_of_normals_workflow): + """Tests PureCnStepPart._get_log_file_create_panel()""" + expected = get_expected_log_files_dict( + base_out="work/{mapper}.purecn/log/{mapper}.purecn.panel_of_normals" + ) + actual = panel_of_normals_workflow.get_log_file("purecn", "create_panel") + assert actual == expected + + +def test_purecn_step_part_get_resource_usage(panel_of_normals_workflow): + """Tests PureCnStepPart.get_resource_usage() for all actions""" + expected = { + "coverage": {"threads": 1, "memory": "24G", "time": "04:00:00"}, + "prepare": {"threads": 1, "memory": "24G", "time": "04:00:00"}, + "create_panel": {"threads": 1, "memory": "24G", "time": "04:00:00"}, + } + for action, resources in expected.items(): + for resource, value in resources.items(): + actual = panel_of_normals_workflow.get_resource("purecn", action, resource) + assert actual == value + + # PanelOfNormalsWorkflow -------------------------------------------------------------------------- def test_panel_of_normals_workflow(panel_of_normals_workflow): """Test simple functionality of the workflow""" # Check created sub steps - expected = ["access", "cnvkit", "link_out", "mutect2"] + expected = ["access", "cnvkit", "link_out", "mutect2", "purecn"] actual = list(sorted(panel_of_normals_workflow.sub_steps.keys())) assert actual == expected @@ -492,6 +631,12 @@ def test_panel_of_normals_workflow(panel_of_normals_workflow): for ext in ("vcf.gz", "vcf.gz.md5", "vcf.gz.tbi", "vcf.gz.tbi.md5") for mapper in ("bwa",) ] + tpl = "output/{mapper}.mutect2/out/{mapper}.mutect2.genomicsDB.{ext}" + expected += [ + tpl.format(mapper=mapper, ext=ext) + for ext in ("tar.gz", "tar.gz.md5") + for mapper in ("bwa",) + ] # add log files tpl = "output/{mapper}.mutect2/log/{mapper}.mutect2.panel_of_normals" for mapper in ("bwa",): @@ -531,6 +676,28 @@ def test_panel_of_normals_workflow(panel_of_normals_workflow): base_out="output/cnvkit.access/log/cnvkit.access" ).values() + # PureCN + tpl = "output/{mapper}.purecn/out/{mapper}.purecn.panel_of_normals.rds{chksum}" + expected += [ + tpl.format(mapper=mapper, chksum=chksum) for mapper in ("bwa",) for chksum in ("", ".md5") + ] + tpl = "output/{mapper}.purecn/out/{mapper}.purecn.mapping_bias.rds{chksum}" + expected += [ + tpl.format(mapper=mapper, chksum=chksum) for mapper in ("bwa",) for chksum in ("", ".md5") + ] + expected += get_expected_log_files_dict( + base_out="output/{mapper}.purecn/log/{mapper}.purecn.panel_of_normals".format(mapper="bwa") + ).values() + tpl = "output/purecn/out/unknown_unknown.{ext}{chksum}" + expected += [ + tpl.format(ext=ext, chksum=chksum) + for ext in ("list", "bed.gz", "bed.gz.tbi") + for chksum in ("", ".md5") + ] + expected += get_expected_log_files_dict( + base_out="output/purecn/log/unknown_unknown".format(mapper="bwa") + ).values() + expected = list(sorted(expected)) actual = list(sorted(panel_of_normals_workflow.get_result_files())) assert actual == expected diff --git a/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals_wgs.py b/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals_wgs.py index 2d785cb67..659f14489 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals_wgs.py +++ b/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals_wgs.py @@ -343,7 +343,7 @@ def test_cnvkit_step_part_get_resource_usage(panel_of_normals_workflow): def test_panel_of_normals_workflow(panel_of_normals_workflow): """Test simple functionality of the workflow""" # Check created sub steps - expected = ["access", "cnvkit", "link_out", "mutect2"] + expected = ["access", "cnvkit", "link_out", "mutect2", "purecn"] actual = list(sorted(panel_of_normals_workflow.sub_steps.keys())) assert actual == expected expected = [] diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py index ff622624c..6704fbfcd 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py @@ -46,10 +46,17 @@ def minimal_config(): - cnvetti_on_target - cnvkit - copywriter + - sequenza + - purecn cnvkit: path_target: /path/to/panel_of_normals/output/cnvkit.target/out/cnvkit.target.bed path_antitarget: /path/to/panel_of_normals/output/cnvkit.antitarget/out/cnvkit.antitarget.bed path_panel_of_normals: /path/to/panel_of_normals/output/bwa.cnvkit.create_panel/out/bwa.cnvkit.panel_of_normals.cnn + purecn: + path_container: /path/to/purecn/container + path_intervals: /path/to/interval/list + path_panel_of_normals: /path/to/purecn/pon + path_mapping_bias: /path/to/mapping/bias data_sets: first_batch: @@ -79,7 +86,10 @@ def somatic_targeted_seq_cnv_calling_workflow( patch_module_fs("snappy_pipeline.workflows.abstract", cancer_sheet_fake_fs, mocker) # Update the "globals" attribute of the mock workflow (snakemake.workflow.Workflow) so we # can obtain paths from the function as if we really had a NGSMappingPipelineStep here - dummy_workflow.globals = {"ngs_mapping": lambda x: "NGS_MAPPING/" + x} + dummy_workflow.globals = { + "ngs_mapping": lambda x: "NGS_MAPPING/" + x, + "somatic_variants": lambda x: "SOMATIC_VARIANT_CALLING/" + x, + } # Construct the workflow object return SomaticTargetedSeqCnvCallingWorkflow( dummy_workflow, @@ -811,13 +821,220 @@ def test_copywriter_step_part_get_resource_usage_call(somatic_targeted_seq_cnv_c assert actual == expected, msg_error +# Tests for SequenzaStepPart ---------------------------------------------------------------------- + + +def test_sequenza_step_part_get_output_files_install(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_output_files() - action 'install'""" + expected = {"done": "work/R_packages/out/sequenza.done"} + actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("sequenza", "install") + assert actual == expected + + +def test_sequenza_step_part_get_log_file_install(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_log_file() - action 'install'""" + base_name = "work/R_packages/log/sequenza" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("sequenza", "install") + assert actual == expected + + +def test_sequenza_step_part_get_output_files_gcreference(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_output_files() - action 'gcreference'""" + expected = {"gc": "work/static_data/out/sequenza.50.wig.gz"} + actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("sequenza", "gcreference") + assert actual == expected + + +def test_sequenza_step_part_get_log_file_gcreference(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_log_file() - action 'gcreference'""" + base_name = "work/static_data/log/sequenza.50" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("sequenza", "gcreference") + assert actual == expected + + +def test_sequenza_step_part_get_input_files_run(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_input_files() - action 'run'""" + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) + expected = { + "gc": "work/static_data/out/sequenza.50.wig.gz", + "normal_bam": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam", + "normal_bai": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam.bai", + "tumor_bam": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam", + "tumor_bai": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam.bai", + } + actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("sequenza", "run")(wildcards) + assert actual == expected + + +def test_sequenza_step_part_get_output_files_run(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_output_files() - action 'run'""" + expected = { + "seqz": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz", + "seqz_md5": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz.md5", + } + actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("sequenza", "run") + assert actual == expected + + +def test_sequenza_step_part_get_log_file_run(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_log_file() - action 'run'""" + base_name = "work/{mapper}.sequenza.{library_name}/log/{mapper}.sequenza.{library_name}.run" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("sequenza", "run") + assert actual == expected + + +def test_sequenza_step_part_get_input_files_report(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_input_files() - action 'report'""" + expected = { + "packages": "work/R_packages/out/sequenza.done", + "seqz": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz", + } + actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("sequenza", "report") + assert actual == expected + + +def test_sequenza_step_part_get_output_files_report(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_output_files() - action 'report'""" + expected = {"done": "work/{mapper}.sequenza.{library_name}/report/.done"} + actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("sequenza", "report") + assert actual == expected + + +def test_sequenza_step_part_get_params_report(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_params() - action 'report'""" + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) + expected = "P001-T1-DNA1-WGS1" + actual = somatic_targeted_seq_cnv_calling_workflow.get_params("sequenza", "report")(wildcards) + assert actual == expected + + +def test_sequenza_step_part_get_log_file_report(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_log_file() - action 'report'""" + base_name = "work/{mapper}.sequenza.{library_name}/log/{mapper}.sequenza.{library_name}.report" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("sequenza", "report") + assert actual == expected + + +def test_sequenza_step_part_get_resource_usage_call(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_resource_usage()""" + # Define expected + expected_dicts = { + "run": {"threads": 4, "time": "24:00:00", "memory": "16G", "partition": "medium"}, + } + # Evaluate + for action, resources in expected_dicts.items(): + for resource, expected in resources.items(): + msg_error = f"Assertion error for resource '{resource}' in '{action}'." + actual = somatic_targeted_seq_cnv_calling_workflow.get_resource( + "sequenza", action, resource + ) + assert actual == expected, msg_error + + +# Tests for PureCNStepPart ---------------------------------------------------------------------- + + +def test_purecn_step_part_get_input_files_coverage(somatic_targeted_seq_cnv_calling_workflow): + """Tests PureCNStepPart.get_input_files() - action 'coverage'""" + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) + expected = { + "bam": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam", + "bai": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam.bai", + } + actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("purecn", "coverage")( + wildcards + ) + assert actual == expected + + +def test_purecn_step_part_get_output_files_coverage(somatic_targeted_seq_cnv_calling_workflow): + """Tests PureCNStepPart.get_output_files() - action 'coverage'""" + expected = { + "coverage": "work/{mapper}.purecn.{library_name}/out/{mapper}.{library_name}_coverage_loess.txt.gz" + } + actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("purecn", "coverage") + assert actual == expected + + +def test_purecn_step_part_get_log_file_coverage(somatic_targeted_seq_cnv_calling_workflow): + """Tests PureCNStepPart.get_log_file() - action 'coverage'""" + base_name = "work/{mapper}.purecn.{library_name}/log/{mapper}.purecn.{library_name}.coverage" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("purecn", "coverage") + assert actual == expected + + +def test_purecn_step_part_get_input_files_run(somatic_targeted_seq_cnv_calling_workflow): + """Tests PureCNStepPart.get_input_files() - action 'run'""" + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) + expected = { + "tumor": "work/bwa.purecn.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1_coverage_loess.txt.gz", + "vcf": "SOMATIC_VARIANT_CALLING/output/bwa.mutect2.P001-T1-DNA1-WGS1/out/bwa.mutect2.P001-T1-DNA1-WGS1.full.vcf.gz", + } + actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("purecn", "run")(wildcards) + assert actual == expected + + +def test_purecn_step_part_get_output_files_run(somatic_targeted_seq_cnv_calling_workflow): + """Tests PureCNStepPart.get_output_files() - action 'run'""" + base_name = "work/{mapper}.purecn.{library_name}/out/{library_name}" + expected = { + "segments": base_name + "_dnacopy.seg", + "ploidy": base_name + ".csv", + "pvalues": base_name + "_amplification_pvalues.csv", + "vcf": base_name + ".vcf.gz", + "vcf_tbi": base_name + ".vcf.gz.tbi", + "loh": base_name + "_loh.csv", + } + expected = {**expected, **{k + "_md5": v + ".md5" for k, v in expected.items()}} + actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("purecn", "run") + assert actual == expected + + +def test_purecn_step_part_get_log_file_run(somatic_targeted_seq_cnv_calling_workflow): + """Tests PureCNStepPart.get_log_file() - action 'run'""" + base_name = "work/{mapper}.purecn.{library_name}/log/{mapper}.purecn.{library_name}.run" + expected = get_expected_log_files_dict(base_out=base_name) + actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("purecn", "run") + assert actual == expected + + +def test_purecn_step_part_get_resource_usage(somatic_targeted_seq_cnv_calling_workflow): + """Tests PureCNStepPart.get_resource_usage()""" + # Define expected + expected_dicts = { + "coverage": {"threads": 1, "time": "04:00:00", "memory": "24G", "partition": "medium"}, + "run": {"threads": 4, "time": "24:00:00", "memory": "96G", "partition": "medium"}, + } + # Evaluate + for action, resources in expected_dicts.items(): + for resource, expected in resources.items(): + msg_error = f"Assertion error for resource '{resource}' in '{action}'." + actual = somatic_targeted_seq_cnv_calling_workflow.get_resource( + "purecn", action, resource + ) + assert actual == expected, msg_error + + # Tests for SomaticTargetedSeqCnvCallingWorkflow -------------------------------------------------- def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_calling_workflow): """Test simple functionality of the workflow""" # Check created sub steps - expected = ["cnvetti_off_target", "cnvetti_on_target", "cnvkit", "copywriter", "link_out"] + expected = [ + "cnvetti_off_target", + "cnvetti_on_target", + "cnvkit", + "copywriter", + "link_out", + "purecn", + "sequenza", + ] actual = list(sorted(somatic_targeted_seq_cnv_calling_workflow.sub_steps.keys())) assert actual == expected @@ -928,6 +1145,31 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call "segments.txt.md5", ) ] + # purecn + tpl = "output/bwa.purecn.P00{i}-T{t}-DNA1-WGS1/out/P00{i}-T{t}-DNA1-WGS1{ext}{checksum}" + expected += [ + tpl.format(i=i, t=t, ext=ext, checksum=checksum) + for i, t in ((1, 1), (2, 1), (2, 2)) + for ext in ( + ".csv", + ".vcf.gz", + ".vcf.gz.tbi", + "_dnacopy.seg", + "_amplification_pvalues.csv", + "_loh.csv", + ) + for checksum in ("", ".md5") + ] + # sequenza + tpl = ( + "output/bwa.sequenza.P00{i}-T{t}-DNA1-WGS1/out/" + "bwa.sequenza.P00{i}-T{t}-DNA1-WGS1.seqz.gz{checksum}" + ) + expected += [ + tpl.format(i=i, t=t, checksum=checksum) + for i, t in ((1, 1), (2, 1), (2, 2)) + for checksum in ("", ".md5") + ] expected = list(sorted(expected)) actual = list(sorted(somatic_targeted_seq_cnv_calling_workflow.get_result_files())) # HACK TODO From 4874074d8200ac33d29377ce1a812dfbb48adc31 Mon Sep 17 00:00:00 2001 From: ericblanc20 Date: Tue, 31 Oct 2023 17:39:27 +0100 Subject: [PATCH 19/19] feat: feature-complete end-to-end run of the Becnel dataset on hs37d5 & GRCh38.d1.vd1 (#460) Co-authored-by: Manuela Benary --- requirements/test.txt | 1 + .../workflows/cbioportal_export/__init__.py | 50 ++-- .../Snakefile | 2 +- .../workflows/ngs_mapping/__init__.py | 60 ++-- .../workflows/panel_of_normals/__init__.py | 11 +- .../somatic_cnv_checking/__init__.py | 3 +- .../somatic_gene_fusion_calling/__init__.py | 5 - .../Snakefile | 41 +-- .../__init__.py | 68 +++-- .../somatic_variant_annotation/Snakefile | 2 +- .../somatic_variant_annotation/__init__.py | 20 +- .../somatic_variant_filtration/__init__.py | 48 +-- .../tumor_mutational_burden/__init__.py | 6 + snappy_wrappers/utils.py | 68 +++++ snappy_wrappers/wrapper_parallel.py | 2 + .../wrappers/arriba/run/wrapper.py | 2 +- .../wrappers/bcftools/TMB/wrapper.py | 61 ++-- snappy_wrappers/wrappers/bwa_mem2/wrapper.py | 2 +- .../cbioportal/clinical_data/wrapper.py | 10 +- .../wrappers/cbioportal/generate_cna/script.R | 7 +- .../cbioportal/generate_cna/wrapper.py | 2 +- .../wrappers/cbioportal/helper_functions.R | 6 +- .../wrappers/cbioportal/merge_tables/script.R | 13 +- .../cbioportal/merge_tables/wrapper.py | 9 +- .../wrappers/cnvkit/export/wrapper.py | 13 +- .../wrappers/cnvkit/postprocess/wrapper.py | 24 +- .../dkfz_bias_filter/environment.yaml | 4 +- .../wrappers/dkfz_bias_filter/wrapper.py | 2 + snappy_wrappers/wrappers/eb_filter/wrapper.py | 15 +- .../wrappers/eb_filter_par/environment.yaml | 2 + .../jannovar/annotate_somatic_vcf/wrapper.py | 8 + .../mutect2_par/run/parallel_mutect2.py | 2 +- .../wrappers/purecn/coverage/wrapper.py | 9 + .../wrappers/purecn/create_panel/wrapper.py | 4 +- .../wrappers/purecn/run/wrapper.py | 46 ++- .../wrappers/scarHRD/environment.yaml | 13 + .../wrappers/scarHRD/install/environment.yaml | 1 + .../wrappers/scarHRD/install/wrapper.py | 22 ++ .../wrappers/scarHRD/run/wrapper.py | 29 +- .../sequenza/coverage/environment.yaml | 1 + .../wrappers/sequenza/coverage/wrapper.py | 72 +++++ .../wrappers/sequenza/environment.yaml | 10 - .../sequenza/gcreference/environment.yaml | 8 +- .../sequenza/install/environment.yaml | 18 ++ .../wrappers/sequenza/install/wrapper.py | 22 ++ .../wrappers/sequenza/report/wrapper.py | 5 +- .../wrappers/sequenza/run/environment.yaml | 2 +- .../wrappers/sequenza/run/wrapper.py | 79 ++++- .../somatic_cnv_checking/cnv-check-plot.R | 5 +- .../wrappers/somatic_cnv_checking/wrapper.py | 2 +- snappy_wrappers/wrappers/star/wrapper.py | 14 +- .../vcf_to_table/protein_mutation_parser.py | 2 +- .../wrappers/vcf2maf/vcf_to_table/wrapper.py | 2 +- .../wrappers/vcfpy/add_bed/wrapper.py | 273 ++++++++++-------- .../test_workflows_cbioportal_export.py | 11 +- .../workflows/test_workflows_ngs_mapping.py | 2 + .../test_workflows_panel_of_normals.py | 10 +- .../test_workflows_somatic_cnv_checking.py | 3 +- ...tic_gene_fusion_calling_processed_fastq.py | 3 +- ...kflows_somatic_targeted_seq_cnv_calling.py | 161 ++++++----- ...st_workflows_somatic_variant_annotation.py | 12 +- ...st_workflows_somatic_variant_filtration.py | 60 ++-- .../wrappers/data/mutect2_par_run.snakemake | 2 +- .../wrappers/test_install_R_package.py | 52 ++++ .../wrappers/test_mutect2_par_run.py | 10 +- 65 files changed, 1009 insertions(+), 525 deletions(-) create mode 120000 snappy_wrappers/wrappers/scarHRD/install/environment.yaml create mode 100644 snappy_wrappers/wrappers/scarHRD/install/wrapper.py create mode 120000 snappy_wrappers/wrappers/sequenza/coverage/environment.yaml create mode 100644 snappy_wrappers/wrappers/sequenza/coverage/wrapper.py delete mode 100644 snappy_wrappers/wrappers/sequenza/environment.yaml mode change 120000 => 100644 snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml create mode 100644 snappy_wrappers/wrappers/sequenza/install/environment.yaml create mode 100644 snappy_wrappers/wrappers/sequenza/install/wrapper.py create mode 100644 tests/snappy_wrappers/wrappers/test_install_R_package.py diff --git a/requirements/test.txt b/requirements/test.txt index b6888285f..78e7bae71 100644 --- a/requirements/test.txt +++ b/requirements/test.txt @@ -5,6 +5,7 @@ pytest coverage pytest-cov pytest-mock +pytest-subprocess # Fake file system for testing pyfakefs diff --git a/snappy_pipeline/workflows/cbioportal_export/__init__.py b/snappy_pipeline/workflows/cbioportal_export/__init__.py index d5889f5c6..94eb89edb 100644 --- a/snappy_pipeline/workflows/cbioportal_export/__init__.py +++ b/snappy_pipeline/workflows/cbioportal_export/__init__.py @@ -77,6 +77,7 @@ cbioportal_export: # Required for RNA expression path_ngs_mapping: "" # When missing, no expression data is uploaded to cBioPortal + mapping_tool: "bwa" expression_tool: "star" # Required for somatic variants path_somatic_variant: ../somatic_variant_filtration # REQUIRED (before or after filtration) @@ -334,7 +335,7 @@ def __init__(self, parent): name_pattern = "{mapper}.{caller}.{annotator}.{{library_name}}" tpl = os.path.join("work/maf", name_pattern, "out", name_pattern + "{ext}") self.input_tpl = tpl.format( - mapper="bwa", + mapper=self.config["mapping_tool"], caller=self.config["somatic_variant_calling_tool"], annotator=self.config["somatic_variant_annotation_tool"], filter_set=self.config["filter_set"], @@ -358,8 +359,12 @@ def get_input_files(self, action): # Validate action self._validate_action(action) name_pattern = "{mapper}.{caller}.{tumor_library}" - yield "cns", os.path.join( - self.config["path_copy_number"], "output", name_pattern, "out", name_pattern + ".cns" + yield "DNAcopy", os.path.join( + self.config["path_copy_number"], + "output", + name_pattern, + "out", + name_pattern + "_dnacopy.seg", ) @dictify @@ -390,10 +395,8 @@ def get_args(self, action): # Validate action self._validate_action(action) return { - "features": self.parent.w_config["step_config"]["ngs_mapping"][ - self.config["expression_tool"] - ]["path_features"], "pipeline_id": "ENSEMBL", + "features": self.parent.w_config["static_data_config"]["features"]["path"], } def get_resource_usage(self, action): @@ -427,7 +430,9 @@ class cbioportalCnaFilesStepPart(cbioportalExportStepPart): def __init__(self, parent): super().__init__(parent) - name_pattern = "bwa." + self.config["copy_number_tool"] + ".{library_name}" + name_pattern = ( + self.config["mapping_tool"] + "." + self.config["copy_number_tool"] + ".{library_name}" + ) self.input_tpl = os.path.join("work/cna", name_pattern, "out", name_pattern + ".cna") def get_args(self, action): @@ -482,9 +487,15 @@ class cbioportalSegmentStepPart(cbioportalExportStepPart): def __init__(self, parent): super().__init__(parent) - name_pattern = "bwa." + self.config["copy_number_tool"] + ".{library_name}" + name_pattern = ( + self.config["mapping_tool"] + "." + self.config["copy_number_tool"] + ".{library_name}" + ) self.input_tpl = os.path.join( - self.config["path_copy_number"], "output", name_pattern, "out", name_pattern + ".cns" + self.config["path_copy_number"], + "output", + name_pattern, + "out", + name_pattern + "_dnacopy.seg", ) def get_resource_usage(self, action): @@ -537,9 +548,7 @@ def get_args(self, action): "action_type": "expression", "extra_args": { "pipeline_id": "ENSEMBL", - "tx_obj": self.parent.w_config["step_config"]["ngs_mapping"][ - self.config["expression_tool"] - ]["path_features"], + "tx_obj": self.parent.w_config["static_data_config"]["features"]["path"], }, } @@ -813,13 +822,16 @@ def get_result_files(self): def check_config(self): """Check config attributes for presence""" msg = [] - if self.config["path_somatic_variant"] and ( - not self.config["somatic_variant_calling_tool"] - or not self.config["somatic_variant_annotation_tool"] - ): - msg += [ - "Somatic variant calling tool and somatic variant annotation tool must be defined" - ] + if self.config["path_somatic_variant"]: + if not self.config["mapping_tool"]: + msg += ["DNA mapping tool must be defined"] + if ( + not self.config["somatic_variant_calling_tool"] + or not self.config["somatic_variant_annotation_tool"] + ): + msg += [ + "Somatic variant calling tool and somatic variant annotation tool must be defined" + ] if self.config["path_copy_number"] and not self.config["copy_number_tool"]: msg += [ "Somatic copy number calling tool must be defined when CNV results are available" diff --git a/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile b/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile index fc8dca2ab..8397821b0 100644 --- a/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile +++ b/snappy_pipeline/workflows/homologous_recombination_deficiency/Snakefile @@ -75,7 +75,7 @@ rule homologous_recombination_deficiency_scarHRD_install: log: **wf.get_log_file("scarHRD", "install"), wrapper: - wf.wrapper_path("r") + wf.wrapper_path("scarHRD/install") rule homologous_recombination_deficiency_scarHRD_run: diff --git a/snappy_pipeline/workflows/ngs_mapping/__init__.py b/snappy_pipeline/workflows/ngs_mapping/__init__.py index 0854f0f4b..3584a8619 100644 --- a/snappy_pipeline/workflows/ngs_mapping/__init__.py +++ b/snappy_pipeline/workflows/ngs_mapping/__init__.py @@ -171,13 +171,18 @@ This removes the need to include gene models into the generation of indices, so that the user can select the gene models (either from ENSEMBL or GENCODE, for example). -When the configuration option `path_features` is set, the step will output a table of expression counts -for all genes, in `output/star.{library_name}/out/star.{library_name}.GeneCounts.tab`. +The computation of gene counts relies on the features defined in the `static_data_config` section of the +configuration file. The other steps relying of feature annotations should use this too. + +`STAR` outputs the counts for unstranded, forward and reverse strand protocols. When the user doesn't supply the +protocol code (0 for unstranded, 1 for forward & 2 for reverse), the step runs `infer_experiment` +(from the `rseqc` library) to infer the protocol strandedness. In both cases, the step generate a copy of +the `STAR` output containing only the relevant column included. This final version of the gene counts is found in +`output/star.{library_name}/out/star.{library_name}.GeneCounts.tab`. If the configuration option `transcriptome` is set to `true`, the step will output a bam file of reads mapped to the transcriptome (`output/stat.{library_name}/out/star.{library_name}.toTranscriptome.bam`). -`STAR` will rely on the `path_features` configuration option, or on the gene models embedded in -the indices to generate the mappings. If both are absent, the step will fail. +As with gene counts, `STAR` will rely on the static data configuration to generate the mappings. Note that the mappings to the transcriptome will not be indexes using `samtools index`, because the absence of the positional mappings. @@ -387,7 +392,6 @@ # Configuration for STAR star: path_index: REQUIRED # Required if listed in ngs_mapping.tools.rna; otherwise, can be removed. - path_features: "" # Required for computing gene counts num_threads_align: 16 num_threads_trimming: 8 num_threads_bam_view: 4 @@ -801,11 +805,10 @@ def check_config(self): def _get_output_files_run_work(self): """Override base class' function to make Snakemake aware of extra files for STAR.""" output_files = super()._get_output_files_run_work() - if self.config[self.name]["path_features"]: - output_files["gene_counts"] = self.base_path_out.format( - mapper=self.name, ext=".GeneCounts.tab" - ) - output_files["gene_counts_md5"] = output_files["gene_counts"] + ".md5" + output_files["gene_counts"] = self.base_path_out.format( + mapper=self.name, ext=".GeneCounts.tab" + ) + output_files["gene_counts_md5"] = output_files["gene_counts"] + ".md5" if self.config[self.name]["transcriptome"]: output_files["transcriptome"] = self.base_path_out.format( mapper=self.name, ext=".toTranscriptome.bam" @@ -900,27 +903,24 @@ def get_output_files(self, action): def get_result_files(self): for mapper in self.config["tools"]["rna"]: - if self.config[mapper]["path_features"]: - tpl_out = ( - "output/{mapper}.{library_name}/out/{mapper}.{library_name}.GeneCounts.tab" - ) - tpl_strandedness = "output/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.decision.json" - tpl_log = ( - "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.{ext}" - ) - for library_name, extra_info in self.parent.ngs_library_to_extra_infos.items(): - if extra_info["extractionType"] == "RNA": - yield tpl_out.format(mapper=mapper, library_name=library_name) - yield tpl_out.format(mapper=mapper, library_name=library_name) + ".md5" - yield tpl_strandedness.format(mapper=mapper, library_name=library_name) - yield tpl_strandedness.format( - mapper=mapper, library_name=library_name + tpl_out = "output/{mapper}.{library_name}/out/{mapper}.{library_name}.GeneCounts.tab" + tpl_strandedness = ( + "output/{mapper}.{library_name}/strandedness/{mapper}.{library_name}.decision.json" + ) + tpl_log = ( + "output/{mapper}.{library_name}/log/{mapper}.{library_name}.strandedness.{ext}" + ) + for library_name, extra_info in self.parent.ngs_library_to_extra_infos.items(): + if extra_info["extractionType"] == "RNA": + yield tpl_out.format(mapper=mapper, library_name=library_name) + yield tpl_out.format(mapper=mapper, library_name=library_name) + ".md5" + yield tpl_strandedness.format(mapper=mapper, library_name=library_name) + yield tpl_strandedness.format(mapper=mapper, library_name=library_name) + ".md5" + for ext in ("log", "conda_info.txt", "conda_list.txt"): + yield tpl_log.format(mapper=mapper, library_name=library_name, ext=ext) + yield tpl_log.format( + mapper=mapper, library_name=library_name, ext=ext ) + ".md5" - for ext in ("log", "conda_info.txt", "conda_list.txt"): - yield tpl_log.format(mapper=mapper, library_name=library_name, ext=ext) - yield tpl_log.format( - mapper=mapper, library_name=library_name, ext=ext - ) + ".md5" @dictify def get_log_file(self, action): diff --git a/snappy_pipeline/workflows/panel_of_normals/__init__.py b/snappy_pipeline/workflows/panel_of_normals/__init__.py index 63b2921e5..b715ab969 100644 --- a/snappy_pipeline/workflows/panel_of_normals/__init__.py +++ b/snappy_pipeline/workflows/panel_of_normals/__init__.py @@ -162,6 +162,7 @@ purecn: path_normals_list: "" # Optional file listing libraries to include in panel path_bait_regions: REQUIRED # Bed files of enrichment kit sequences (MergedProbes for Agilent SureSelect), recommended by PureCN author + path_genomicsDB: REQUIRED # Mutect2 genomicsDB created during panel_of_normals genome_name: "unknown" # Must be one from hg18, hg19, hg38, mm9, mm10, rn4, rn5, rn6, canFam3 enrichment_kit_name: "unknown" # For filename only... mappability: "" # GRCh38: /fast/work/groups/cubi/projects/biotools/static_data/app_support/PureCN/hg38/mappability.bw @@ -259,19 +260,19 @@ def get_input_files(self, action): @dictify def _get_input_files_coverage(self, wildcards): yield "container", "work/containers/out/purecn.simg" - tpl = "output/{mapper}.{normal_library}/out/{mapper}.{normal_library}.bam" yield "intervals", "work/purecn/out/{}_{}.list".format( self.config["purecn"]["enrichment_kit_name"], self.config["purecn"]["genome_name"], ) + tpl = "output/{mapper}.{library_name}/out/{mapper}.{library_name}.bam" yield "bam", self.ngs_mapping(tpl.format(**wildcards)) @dictify def _get_input_files_create(self, wildcards): yield "container", "work/containers/out/purecn.simg" - tpl = "work/{mapper}.purecn/out/{mapper}.{normal_library}_coverage_loess.txt.gz" + tpl = "work/{mapper}.purecn/out/{mapper}.purecn.{library_name}_coverage_loess.txt.gz" yield "normals", [ - tpl.format(mapper=wildcards.mapper, normal_library=lib) for lib in self.normal_libraries + tpl.format(mapper=wildcards.mapper, library_name=lib) for lib in self.normal_libraries ] def get_output_files(self, action): @@ -294,7 +295,7 @@ def get_output_files(self, action): } if action == "coverage": return { - "coverage": "work/{mapper}.purecn/out/{mapper}.{normal_library,.+-DNA[0-9]+-WES[0-9]+}_coverage_loess.txt.gz" + "coverage": "work/{mapper}.purecn/out/{mapper}.purecn.{library_name,.+-DNA[0-9]+-WES[0-9]+}_coverage_loess.txt.gz" } if action == "create_panel": return { @@ -314,7 +315,7 @@ def get_log_file(self, action): self.config["purecn"]["enrichment_kit_name"], self.config["purecn"]["genome_name"], ), - "coverage": "work/{mapper}.purecn/log/{mapper}.{normal_library,.+-DNA[0-9]+-WES[0-9]+}", + "coverage": "work/{mapper}.purecn/log/{mapper}.purecn.{library_name,.+-DNA[0-9]+-WES[0-9]+}", "create_panel": "work/{mapper}.purecn/log/{mapper}.purecn.panel_of_normals", } assert action in self.actions diff --git a/snappy_pipeline/workflows/somatic_cnv_checking/__init__.py b/snappy_pipeline/workflows/somatic_cnv_checking/__init__.py index f5781c417..521807961 100644 --- a/snappy_pipeline/workflows/somatic_cnv_checking/__init__.py +++ b/snappy_pipeline/workflows/somatic_cnv_checking/__init__.py @@ -212,8 +212,7 @@ def input_function(wildcards): base_path = "output/{mapper}.{caller}.{library_name}/out/{mapper}.{caller}.{library_name}".format( **wildcards ) - filenames["cnv"] = cnv_calling(base_path + ".bed.gz") - filenames["cnv_tbi"] = filenames["cnv"] + ".tbi" + filenames["cnv"] = cnv_calling(base_path + "_dnacopy.seg") return filenames return input_function diff --git a/snappy_pipeline/workflows/somatic_gene_fusion_calling/__init__.py b/snappy_pipeline/workflows/somatic_gene_fusion_calling/__init__.py index b9974929f..0275f57b8 100644 --- a/snappy_pipeline/workflows/somatic_gene_fusion_calling/__init__.py +++ b/snappy_pipeline/workflows/somatic_gene_fusion_calling/__init__.py @@ -90,7 +90,6 @@ path_dataset_directory: REQUIRED arriba: path_index: REQUIRED # REQUIRED STAR path index (preferably 2.7.10 or later) - features: REQUIRED # REQUIRED Gene features (for ex. ENCODE or ENSEMBL) in gtf format blacklist: "" # optional (provided in the arriba distribution, see /fast/work/groups/cubi/projects/biotools/static_data/app_support/arriba/v2.3.0) known_fusions: "" # optional tags: "" # optional (can be set to the same path as known_fusions) @@ -423,10 +422,6 @@ def check_config(self): config_keys=("step_config", "somatic_gene_fusion_calling", "arriba", "path_index"), msg="Path to STAR indices is required", ) - self.parent.ensure_w_config( - config_keys=("step_config", "somatic_gene_fusion_calling", "arriba", "features"), - msg="Path to genomic features gtf file is required", - ) # Check that the path to the STAR index is valid. for fn in ("Genome", "SA", "SAindex"): diff --git a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/Snakefile b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/Snakefile index 330476306..569ecd7df 100644 --- a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/Snakefile +++ b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/Snakefile @@ -244,6 +244,7 @@ rule somatic_targeted_seq_cnv_calling_sequenza_install: params: packages=[ {"name": "aroneklund/copynumber", "repo": "github"}, + {"name": "sequenzatools/sequenza", "repo": "bitbucket"}, ], threads: wf.get_resource("sequenza", "install", "threads") resources: @@ -254,7 +255,7 @@ rule somatic_targeted_seq_cnv_calling_sequenza_install: log: **wf.get_log_file("sequenza", "install"), wrapper: - wf.wrapper_path("r") + wf.wrapper_path("sequenza/install") rule somatic_targeted_seq_cnv_calling_sequenza_gcreference: @@ -272,6 +273,25 @@ rule somatic_targeted_seq_cnv_calling_sequenza_gcreference: wf.wrapper_path("sequenza/gcreference") +rule somatic_targeted_seq_cnv_calling_sequenza_coverage: + input: + unpack(wf.get_input_files("sequenza", "coverage")), + output: + **wf.get_output_files("sequenza", "coverage"), + params: + sample_id=wf.get_params("sequenza", "coverage"), + threads: wf.get_resource("sequenza", "coverage", "threads") + resources: + time=wf.get_resource("sequenza", "coverage", "time"), + memory=wf.get_resource("sequenza", "coverage", "memory"), + partition=wf.get_resource("sequenza", "coverage", "partition"), + tmpdir=wf.get_resource("sequenza", "coverage", "tmpdir"), + log: + **wf.get_log_file("sequenza", "coverage"), + wrapper: + wf.wrapper_path("sequenza/coverage") + + rule somatic_targeted_seq_cnv_calling_sequenza_run: input: unpack(wf.get_input_files("sequenza", "run")), @@ -289,25 +309,6 @@ rule somatic_targeted_seq_cnv_calling_sequenza_run: wf.wrapper_path("sequenza/run") -rule somatic_targeted_seq_cnv_calling_sequenza_report: - input: - **wf.get_input_files("sequenza", "report"), - output: - **wf.get_output_files("sequenza", "report"), - params: - sample_id=wf.get_params("sequenza", "report"), - threads: wf.get_resource("sequenza", "report", "threads") - resources: - time=wf.get_resource("sequenza", "report", "time"), - memory=wf.get_resource("sequenza", "report", "memory"), - partition=wf.get_resource("sequenza", "report", "partition"), - tmpdir=wf.get_resource("sequenza", "report", "tmpdir"), - log: - **wf.get_log_file("sequenza", "report"), - wrapper: - wf.wrapper_path("sequenza/report") - - # Run PureCN ------------------------------------------------------ diff --git a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py index 91d708894..a7cf820bd 100644 --- a/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py +++ b/snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/__init__.py @@ -476,16 +476,21 @@ class SequenzaStepPart(SomaticTargetedSeqCnvCallingStepPart): actions = ( "install", "gcreference", + "coverage", "run", - "report", ) #: Class resource usage dictionary. Key: action type (string); Value: resource (ResourceUsage). resource_usage = { + "coverage": ResourceUsage( + threads=1, + time="24:00:00", # 1 day + memory="24G", + ), "run": ResourceUsage( threads=4, time="24:00:00", # 1 day - memory="16G", + memory="64G", ), } @@ -498,12 +503,12 @@ def get_input_files(self, action): self._validate_action(action) method_mapping = { + "coverage": self._get_input_files_coverage(), "run": self._get_input_files_run(), - "report": self._get_input_files_report(), } return method_mapping[action] - def _get_input_files_run(self): + def _get_input_files_coverage(self): @dictify def input_function(wildcards): ngs_mapping = self.parent.sub_workflows["ngs_mapping"] @@ -525,11 +530,14 @@ def input_function(wildcards): return input_function - def _get_input_files_report(self): - return { - "packages": "work/R_packages/out/sequenza.done", - "seqz": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz", - } + def _get_input_files_run(self): + @dictify + def input_function(wildcards): + yield "packages", "work/R_packages/out/sequenza.done" + name_pattern = "{mapper}.sequenza.{library_name}" + yield "seqz", f"work/{name_pattern}/out/{name_pattern}.seqz.gz" + + return input_function def get_output_files(self, action): if action == "install": @@ -540,13 +548,19 @@ def get_output_files(self, action): length=self.config["sequenza"]["length"], ) } + elif action == "coverage": + name_pattern = "{mapper}.sequenza.{library_name}" + return { + "seqz": f"work/{name_pattern}/out/{name_pattern}.seqz.gz", + "seqz_md5": f"work/{name_pattern}/out/{name_pattern}.seqz.gz.md5", + } elif action == "run": + name_pattern = "{mapper}.sequenza.{library_name}" return { - "seqz": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz", - "seqz_md5": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz.md5", + "seg": f"work/{name_pattern}/out/{name_pattern}_dnacopy.seg", + "seg_md5": f"work/{name_pattern}/out/{name_pattern}_dnacopy.seg.md5", + "done": f"work/{name_pattern}/report/.done", } - elif action == "report": - return {"done": "work/{mapper}.sequenza.{library_name}/report/.done"} else: raise UnsupportedActionException( "Action '{action}' is not supported. Valid options: {valid}".format( @@ -616,8 +630,8 @@ def _get_input_files_run(self, wildcards): "work", name_pattern, "out", - "{mapper}.{library_name}_coverage_loess.txt.gz".format(**wildcards), - ) + name_pattern + "_coverage_loess.txt.gz", + ).format(**wildcards) name_pattern = "{mapper}.{caller}.{library_name}".format( caller=self.config["purecn"]["somatic_variant_caller"], **wildcards, @@ -639,13 +653,9 @@ def get_output_files(self, action): # Validate action self._validate_action(action) name_pattern = "{mapper}.purecn.{library_name}" - prefix = os.path.join("work", name_pattern, "out", "{library_name}") + prefix = os.path.join("work", name_pattern, "out", name_pattern) action_mapping = { - "coverage": { - "coverage": os.path.join( - "work", name_pattern, "out", "{mapper}.{library_name}_coverage_loess.txt.gz" - ) - }, + "coverage": {"coverage": prefix + "_coverage_loess.txt.gz"}, "run": { "segments": prefix + "_dnacopy.seg", "ploidy": prefix + ".csv", @@ -884,12 +894,10 @@ def _get_output_files_call(): @staticmethod def _get_output_files_postprocess(): name_pattern = "{mapper}.cnvkit.{library_name}" - tpl = os.path.join("work", name_pattern, "out", name_pattern + ".bed.gz") + tpl = os.path.join("work", name_pattern, "out", name_pattern + "_dnacopy.seg") return { "final": tpl, - "final_tbi": tpl + ".tbi", "final_md5": tpl + ".md5", - "final_tbi_md5": tpl + ".tbi.md5", } @dictify @@ -920,7 +928,13 @@ def _get_output_files_plot(self): @staticmethod def _get_output_files_export(): - exports = (("seg", "seg"), ("vcf", "vcf.gz"), ("tbi", "vcf.gz.tbi")) + exports = ( + ("bed", "bed.gz"), + ("bed_tbi", "bed.gz.tbi"), + ("seg", "seg"), + ("vcf", "vcf.gz"), + ("vcf_tbi", "vcf.gz.tbi"), + ) output_files = {} tpl = ( "work/{{mapper}}.cnvkit.{{library_name}}/out/" @@ -1148,7 +1162,7 @@ def get_result_files(self): """Return list of result files for the somatic targeted sequencing CNV calling step""" tool_actions = { "cnvkit": ["fix", "postprocess", "report", "export"], - "sequenza": ("run",), + "sequenza": ("coverage", "run"), "purecn": ("run",), "copywriter": ("call",), "cnvetti_on_target": ("coverage", "segment", "postprocess"), @@ -1185,7 +1199,7 @@ def get_result_files(self): library_name=[sample_pair.tumor_sample.dna_ngs_library.name], ) for f in filenames: - if ".tmp." not in f and not f.endswith("/.done"): + if ".tmp." not in f: yield f.replace("work/", "output/") def check_config(self): diff --git a/snappy_pipeline/workflows/somatic_variant_annotation/Snakefile b/snappy_pipeline/workflows/somatic_variant_annotation/Snakefile index a0dd7e158..7fb41ff1d 100644 --- a/snappy_pipeline/workflows/somatic_variant_annotation/Snakefile +++ b/snappy_pipeline/workflows/somatic_variant_annotation/Snakefile @@ -76,7 +76,7 @@ rule somatic_variant_annotation_vep: # Run Jannovar ---------------------------------------------------------------- -rule somatic_variant_annotation_jannovar_annotate_somatic_vcf: +rule somatic_variant_annotation_jannovar: input: **wf.get_input_files("jannovar", "annotate_somatic_vcf"), output: diff --git a/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py b/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py index df2a2d6f7..010ed979a 100644 --- a/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py +++ b/snappy_pipeline/workflows/somatic_variant_annotation/__init__.py @@ -249,7 +249,7 @@ class JannovarAnnotateSomaticVcfStepPart(AnnotateSomaticVcfStepPart): name = "jannovar" #: Annotator name to construct output paths - annotator = "jannovar_annotate_somatic_vcf" + annotator = "jannovar" #: Class available actions actions = ("annotate_somatic_vcf",) @@ -371,12 +371,7 @@ def get_result_files(self): We will process all primary DNA libraries and perform joint calling within pedigrees """ - annotators = list( - map( - lambda x: x.replace("jannovar", "jannovar_annotate_somatic_vcf"), - set(self.config["tools"]) & set(ANNOTATION_TOOLS), - ) - ) + annotators = set(self.config["tools"]) & set(ANNOTATION_TOOLS) callers = set(self.config["tools_somatic_variant_calling"]) name_pattern = "{mapper}.{caller}.{annotator}.{tumor_library.name}" yield from self._yield_result_files_matched( @@ -402,13 +397,10 @@ def get_result_files(self): ) # Annotators with full output full = list( - map( - lambda x: x.replace("jannovar", "jannovar_annotate_somatic_vcf"), - filter( - lambda x: self.sub_steps[x].has_full, - set(self.config["tools"]) & set(ANNOTATION_TOOLS), - ), - ) + filter( + lambda x: self.sub_steps[x].has_full, + set(self.config["tools"]) & set(ANNOTATION_TOOLS), + ), ) yield from self._yield_result_files_matched( os.path.join("output", name_pattern, "out", name_pattern + ".full{ext}"), diff --git a/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py b/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py index 9afe4989a..f5cfcc00e 100644 --- a/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py +++ b/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py @@ -64,7 +64,10 @@ ResourceUsage, ) from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow -from snappy_pipeline.workflows.somatic_variant_annotation import SomaticVariantAnnotationWorkflow +from snappy_pipeline.workflows.somatic_variant_annotation import ( + ANNOTATION_TOOLS, + SomaticVariantAnnotationWorkflow, +) from snappy_pipeline.workflows.somatic_variant_calling import ( SOMATIC_VARIANT_CALLERS_MATCHED, SomaticVariantCallingWorkflow, @@ -87,6 +90,7 @@ path_ngs_mapping: ../ngs_mapping tools_ngs_mapping: null tools_somatic_variant_calling: null + tools_somatic_variant_annotation: null filter_sets: # no_filter: no_filters # implicit, always defined dkfz_only: '' # empty @@ -135,7 +139,7 @@ class SomaticVariantFiltrationStepPart(BaseStepPart): def __init__(self, parent): super().__init__(parent) self.log_path = ( - r"work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + r"work/{mapper}.{var_caller}.{annotator}." r"dkfz_bias_filter.{tumor_library,[^\.]+}/log/snakemake.dkfz_bias_filter.log" ) # Build shortcut from cancer bio sample name to matched cancer sample @@ -201,10 +205,7 @@ class DkfzBiasFilterStepPart(SomaticVariantFiltrationStepPart): def __init__(self, parent): super().__init__(parent) - self.token = ( - "{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." - "dkfz_bias_filter.{tumor_library}" - ) + self.token = "{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.{tumor_library}" @dictify def get_input_files(self, action): @@ -213,8 +214,8 @@ def get_input_files(self, action): self._validate_action(action) # VCF file and index tpl = ( - "output/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.{tumor_library}/out/" - "{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.{tumor_library}" + "output/{mapper}.{var_caller}.{annotator}.{tumor_library}/out/" + "{mapper}.{var_caller}.{annotator}.{tumor_library}" ) key_ext = {"vcf": ".vcf.gz", "vcf_tbi": ".vcf.gz.tbi"} variant_annotation = self.parent.sub_workflows["somatic_variant_annotation"] @@ -233,9 +234,9 @@ def get_output_files(self, action): # Validate action self._validate_action(action) prefix = ( - r"work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + r"work/{mapper}.{var_caller}.{annotator}." r"dkfz_bias_filter.{tumor_library,[^\.]+}/out/{mapper}.{var_caller}." - r"jannovar_annotate_somatic_vcf.dkfz_bias_filter.{tumor_library}" + r"{annotator}.dkfz_bias_filter.{tumor_library}" ) key_ext = { "vcf": ".vcf.gz", @@ -274,10 +275,7 @@ class EbFilterStepPart(SomaticVariantFiltrationStepPart): def __init__(self, parent): super().__init__(parent) - self.token = ( - "{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." - "dkfz_bias_filter.eb_filter.{tumor_library}" - ) + self.token = "{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.eb_filter.{tumor_library}" def get_input_files(self, action): # Validate action @@ -288,9 +286,9 @@ def get_input_files(self, action): def _get_input_files_run(self, wildcards): # VCF file and index tpl = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + "work/{mapper}.{var_caller}.{annotator}." "dkfz_bias_filter.{tumor_library}/out/{mapper}.{var_caller}." - "jannovar_annotate_somatic_vcf.dkfz_bias_filter." + "{annotator}.dkfz_bias_filter." "{tumor_library}" ) key_ext = {"vcf": ".vcf.gz", "vcf_tbi": ".vcf.gz.tbi"} @@ -318,9 +316,9 @@ def get_output_files(self, action): @dictify def _get_output_files_run(self): prefix = ( - r"work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + r"work/{mapper}.{var_caller}.{annotator}." r"dkfz_bias_filter.eb_filter.{tumor_library,[^\.]+}/out/" - r"{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + r"{mapper}.{var_caller}.{annotator}." r"dkfz_bias_filter.eb_filter.{tumor_library}" ) key_ext = { @@ -393,7 +391,7 @@ class ApplyFiltersStepPartBase(SomaticVariantFiltrationStepPart): def __init__(self, parent): super().__init__(parent) name_pattern = ( - "{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + "{mapper}.{var_caller}.{annotator}." "dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}.{exon_list}" ) self.base_path_out = os.path.join("work", name_pattern, "out", name_pattern + "{ext}") @@ -440,9 +438,9 @@ def get_input_files(self, action): # Validate action self._validate_action(action) tpl = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + "work/{mapper}.{var_caller}.{annotator}." "dkfz_bias_filter.eb_filter.{tumor_library}/out/{mapper}.{var_caller}." - "jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." + "{annotator}.dkfz_bias_filter.eb_filter." "{tumor_library}" ) key_ext = {"vcf": ".vcf.gz", "vcf_tbi": ".vcf.gz.tbi"} @@ -554,6 +552,10 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) self.config["tools_somatic_variant_calling"] = self.w_config["step_config"][ "somatic_variant_calling" ]["tools"] + if not self.config["tools_somatic_variant_annotation"]: + self.config["tools_somatic_variant_annotation"] = self.w_config["step_config"][ + "somatic_variant_annotation" + ]["tools"] @listify def get_result_files(self): @@ -561,8 +563,9 @@ def get_result_files(self): Process all primary DNA libraries and perform pairwise calling for tumor/normal pairs """ callers = set(self.config["tools_somatic_variant_calling"]) + annotators = set(self.config["tools_somatic_variant_annotation"]) name_pattern = ( - "{mapper}.{caller}.jannovar_annotate_somatic_vcf." + "{mapper}.{caller}.{annotator}." "dkfz_bias_filter.eb_filter.{tumor_library.name}." "{filter_set}.{exon_list}" ) @@ -574,6 +577,7 @@ def get_result_files(self): os.path.join("output", name_pattern, "out", name_pattern + "{ext}"), mapper=self.config["tools_ngs_mapping"], caller=callers & set(SOMATIC_VARIANT_CALLERS_MATCHED), + annotator=annotators & set(ANNOTATION_TOOLS), filter_set=filter_sets, exon_list=exon_lists, ext=EXT_VALUES, diff --git a/snappy_pipeline/workflows/tumor_mutational_burden/__init__.py b/snappy_pipeline/workflows/tumor_mutational_burden/__init__.py index 0880ba37f..e18d6cfd1 100644 --- a/snappy_pipeline/workflows/tumor_mutational_burden/__init__.py +++ b/snappy_pipeline/workflows/tumor_mutational_burden/__init__.py @@ -196,6 +196,12 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) self.w_config["step_config"]["tumor_mutational_burden"][ "tools_somatic_variant_calling" ] = self.w_config["step_config"]["somatic_variant_calling"]["tools"] + if not self.w_config["step_config"]["tumor_mutational_burden"][ + "tools_somatic_variant_annotation" + ]: + self.w_config["step_config"]["tumor_mutational_burden"][ + "tools_somatic_variant_annotation" + ] = self.w_config["step_config"]["somatic_variant_annotation"]["tools"] @listify def get_result_files(self): diff --git a/snappy_wrappers/utils.py b/snappy_wrappers/utils.py index 1c40143b7..43f8f04b5 100644 --- a/snappy_wrappers/utils.py +++ b/snappy_wrappers/utils.py @@ -2,6 +2,8 @@ """Utility code for snappy_wrappers""" import os +import re +import subprocess __author__ = "Manuel Holtgrewe " @@ -53,3 +55,69 @@ def patched(*args, **kwargs): return dict(gen(*args, **kwargs)) return patched + + +def install_R_package(dest: str, name: str, repo: str): + """Installs R package in directory + + can be on of "cran", "bioconductor", "github", "bitbucket" or "local". + + Github & bitbucket packages can be further defined in the , + choosing a commit, a tag or a pull request (see the remotes package reference). + For local packages, the must be the path to the package source. + + In these cases, the routine tries to be clever and guess the package name from + the . It implements the following recipes: + + - basename of the path without (tar/zip) extension for local packages + - remove username, subdirectory and reference/release/pull request for github & bitbucket + + When installation isn't successful, a subprocess.CalledProcessError is raised + """ + + assert repo in ( + "cran", + "bioconductor", + "github", + "bitbucket", + "local", + ), f"Unknown/unimplemented repository {repo}" + + os.makedirs(os.path.dirname(dest), mode=0o750, exist_ok=True) + + if repo == "cran": + install_cmd = f"install.packages('{name}', lib='{dest}', update=FALSE, ask=FALSE)" + elif repo == "bioconductor": + install_cmd = f"BiocManager::install('{name}', lib='{dest}', update=FALSE, ask=FALSE)" + elif repo == "github": + path = name + pattern = re.compile("^([^/]+)/([^/]+)(/[^@|]+)?([@|].+)?$") + m = pattern.match(path) + assert m, f"Cannot extract package name from github path {path}" + name = m.groups()[1] + install_cmd = f"remotes::install_github('{path}', lib='{dest}', upgrade='never')" + elif repo == "bitbucket": + path = name + pattern = re.compile("^([^/]+)/([^/]+)([/@].+)?$") + m = pattern.match(path) + assert m, f"Cannot extract package name from bitbucket path {path}" + name = m.groups()[1] + install_cmd = f"remotes::install_bitbucket('{path}', lib='{dest}', upgrade='never')" + elif repo == "local": + path = name + pattern = re.compile("^(.+?)(\\.(zip|tar(\\.(gz|bz2))?|tgz2?|tbz))?$") + m = pattern.match(os.path.basename(path)) + assert m, f"Cannot extract package name from local filesystem path {path}" + name = m.groups()[0] + install_cmd = f"remotes::install_local('{path}', lib='{dest}', upgrade='never')" + else: + install_cmd = None + + R_script = [ + install_cmd, + f"status <- try(find.package('{name}', lib.loc='{dest}', quiet=FALSE, verbose=TRUE))", + "status <- ifelse(is(status, 'try-error'), 1, 0)", + "quit(save='no', status=status, runLast=FALSE)", + ] + cmd = ["R", "--vanilla", "-e", "; ".join(R_script)] + return subprocess.run(cmd, text=True, check=True) diff --git a/snappy_wrappers/wrapper_parallel.py b/snappy_wrappers/wrapper_parallel.py index 00f56837e..4b1a8289f 100644 --- a/snappy_wrappers/wrapper_parallel.py +++ b/snappy_wrappers/wrapper_parallel.py @@ -314,6 +314,8 @@ def write_snakemake_debug_helper( :type max_status_checks_per_second: str """ with open(os.path.join(os.getcwd(), "snakemake_call.sh"), "wt") as f_call: + print("/bin/bash") + print("#SBATCH --output {}/slurm_log/%x-%J.log".format(os.getcwd())) print( " ".join( map( diff --git a/snappy_wrappers/wrappers/arriba/run/wrapper.py b/snappy_wrappers/wrappers/arriba/run/wrapper.py index 2c078eea3..e1c9a88e3 100644 --- a/snappy_wrappers/wrappers/arriba/run/wrapper.py +++ b/snappy_wrappers/wrappers/arriba/run/wrapper.py @@ -75,7 +75,7 @@ -x /dev/stdin \ -o $TMPDIR/fusions.tsv -O $TMPDIR/fusions.discarded.tsv \ -a {snakemake.config[static_data_config][reference][path]} \ - -g {snakemake.config[step_config][somatic_gene_fusion_calling][arriba][features]} \ + -g {snakemake.config[static_data_config][features][path]} \ $(if [[ -n "{snakemake.config[step_config][somatic_gene_fusion_calling][arriba][blacklist]}" ]]; then \ echo -b {snakemake.config[step_config][somatic_gene_fusion_calling][arriba][blacklist]} fi) \ diff --git a/snappy_wrappers/wrappers/bcftools/TMB/wrapper.py b/snappy_wrappers/wrappers/bcftools/TMB/wrapper.py index f4ab3db0b..9a381b346 100644 --- a/snappy_wrappers/wrappers/bcftools/TMB/wrapper.py +++ b/snappy_wrappers/wrappers/bcftools/TMB/wrapper.py @@ -7,9 +7,14 @@ __author__ = "Pham Gia Cuong" __email__ = "pham.gia-cuong@bih-charite.de" +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step] + missense_re = ( snakemake.params.args["missense_re"] - if "args" in snakemake.params.keys() and "missense_re" in snakemake.params.args.keys() + if "args" in snakemake.params.keys() + and "missense_re" in snakemake.params.args.keys() + and config["has_annotation"] == "TRUE" else "" ) @@ -25,14 +30,18 @@ conda list > {snakemake.log.conda_list} conda info > {snakemake.log.conda_info} -bed_file={snakemake.config[step_config][tumor_mutational_burden][target_regions]} +bed_file={config[target_regions]} bed_file_name=$(basename $bed_file) bed_md5=$(md5sum $bed_file | awk '{{print $1}}') name_vcf=$(basename {snakemake.input.vcf}) vcf_md5=$(md5sum {snakemake.input.vcf} | awk '{{print $1}}') -total_exom_length=$(zcat $bed_file | \ +# Avoids script failing with gzip error status +cmd=zcat +gzip -t $bed_file || cmd=cat + +total_exom_length=$($cmd $bed_file | \ awk '{{dis+=$3-$2}} END {{print dis}}') #TMB_rounded=`printf "%.3f" $TMB` number_snvs=$(bcftools view -R $bed_file -v snps --threads 2 -H {snakemake.input.vcf}| wc -l) @@ -41,47 +50,45 @@ if [[ -n "{missense_re}" ]] then - number_missense_variants=$(bcftools view -R $bed_file --threads 2 -H {snakemake.input.vcf}| grep -E '{missense_re}' | wc -l) + number_missense_variants=$(bcftools view -R $bed_file --threads 2 -H {snakemake.input.vcf} | grep -E '{missense_re}' | wc -l || true) +else + number_missense_variants=0 fi -TMB=`echo "1000000*($number_variants/$total_exom_length)" | bc -l ` -missense_TMB=`echo "1000000*($number_missense_variants/$total_exom_length)" | bc -l ` -if [[ {snakemake.config[step_config][tumor_mutational_burden][has_annotation]} == "TRUE" ]] +TMB=$(printf "%f" $(echo "1000000*($number_variants/$total_exom_length)" | bc -l)) +missense_TMB=$(printf "%f" $(echo "1000000*($number_missense_variants/$total_exom_length)" | bc -l)) +if [[ {config[has_annotation]} == "TRUE" ]] then - out_file=$(cat << EOF - {{ - "Library_name": {snakemake.wildcards.tumor_library}, - "VCF_file": $name_vcf, - "VCF_md5": $vcf_md5, - "BED_file": $bed_file_name, - "BED_md5": $bed_md5, + cat << EOF > {snakemake.output.json} +{{ + "Library_name": "{snakemake.wildcards.tumor_library}", + "VCF_file": "$name_vcf", + "VCF_md5": "$vcf_md5", + "BED_file": "$bed_file_name", + "BED_md5": "$bed_md5", "TMB": $TMB, "missense_TMB": $missense_TMB, "Number_variants": $number_variants, "Number_snvs": $number_snvs, "Number_indels": $number_indels, "Total_regions_length": $total_exom_length - }} +}} EOF - ) - echo $out_file > {snakemake.output.json} else - out_file=$(cat << EOF - {{ - "Library_name": {snakemake.wildcards.tumor_library}, - "VCF_file": $name_vcf, - "VCF_md5": $vcf_md5, - "BED_file": $bed_file_name, - "BED_md5": $bed_md5, + cat << EOF > {snakemake.output.json} +{{ + "Library_name": "{snakemake.wildcards.tumor_library}", + "VCF_file": "$name_vcf", + "VCF_md5": "$vcf_md5", + "BED_file": "$bed_file_name", + "BED_md5": "$bed_md5", "TMB": $TMB, "Number_variants": $number_variants, "Number_snvs": $number_snvs, "Number_indels": $number_indels, "Total_regions_length": $total_exom_length - }} +}} EOF - ) - echo $out_file > {snakemake.output.json} fi pushd $(dirname {snakemake.output.json}) diff --git a/snappy_wrappers/wrappers/bwa_mem2/wrapper.py b/snappy_wrappers/wrappers/bwa_mem2/wrapper.py index 2b11850ff..7196322ff 100644 --- a/snappy_wrappers/wrappers/bwa_mem2/wrapper.py +++ b/snappy_wrappers/wrappers/bwa_mem2/wrapper.py @@ -78,7 +78,7 @@ set -x if [[ "{snakemake.config[step_config][ngs_mapping][bwa_mem2][trim_adapters]}" == "True" ]]; then - trimadapt-mt -p {snakemake.config[step_config][ngs_mapping][bwa_mem2][num_threads_trimming]} + trimadap-mt -p {snakemake.config[step_config][ngs_mapping][bwa_mem2][num_threads_trimming]} else cat fi diff --git a/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py b/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py index 38788eacf..3380dbe6f 100644 --- a/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py +++ b/snappy_wrappers/wrappers/cbioportal/clinical_data/wrapper.py @@ -49,7 +49,10 @@ class SampleInfoTMB: column = "TMB" def __init__(self, config, **kwargs): - name_pattern = "bwa." + kwargs["somatic_variant_tool"] + ".tmb.{library}" + name_pattern = "bwa." + kwargs["somatic_variant_tool"] + if kwargs["somatic_variant_annotation_tool"]: + name_pattern += "." + kwargs["somatic_variant_annotation_tool"] + name_pattern += ".tmb.{library}" self.tpl = os.path.join( config["path"], "output", name_pattern, "out", name_pattern + ".json" ) @@ -61,7 +64,7 @@ def get_data(self, lib_by_extraction): try: with open(path, "r") as f: result = json.load(f) - return result["TMB"] + return result.get("missense_TMB", result["TMB"]) except Exception as e: print( "WARNING- error {} occured when extraction TMB for library {}".format( @@ -87,6 +90,9 @@ def write_clinical_samples_tsv(donors): SampleInfoTMB( extra_info, somatic_variant_tool=config["somatic_variant_calling_tool"], + somatic_variant_annotation_tool=config.get( + "somatic_variant_annotation_tool", None + ), ) ) else: diff --git a/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R b/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R index 87fe716ae..480942d83 100644 --- a/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R +++ b/snappy_wrappers/wrappers/cbioportal/generate_cna/script.R @@ -13,10 +13,9 @@ cns_to_cna <- function(fn, tx_obj=TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapie stopifnot("gene_id" %in% colnames(GenomicRanges::mcols(genes))) segments <- read.table(fn, sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE) - if ("chromosome" %in% colnames(segments)) colnames(segments)[colnames(segments)=="chromosome"] <- "chrom" - stopifnot(all(c("cn", "log2", "chrom", "start", "end") %in% colnames(segments))) + stopifnot(all(c("chrom", "loc.start", "loc.end", "seg.mean", "C") %in% colnames(segments))) - seg <- GenomicRanges::makeGRangesFromDataFrame(segments, seqnames.field="chrom", start.field="start", end.field="end", strand="*", keep.extra.columns=FALSE) + seg <- GenomicRanges::makeGRangesFromDataFrame(segments, seqnames.field="chrom", start.field="loc.start", end.field="loc.end", strand="*", keep.extra.columns=FALSE) i <- GenomicRanges::findOverlaps(genes, seg) i <- split(S4Vectors::subjectHits(i), S4Vectors::queryHits(i)) @@ -24,7 +23,7 @@ cns_to_cna <- function(fn, tx_obj=TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapie tbl <- data.frame(FeatureID=as.character(genes$gene_id), cn=NA, log2=NA) colnames(tbl)[1] <- pipeline_id - tbl[as.numeric(names(i)),c("cn", "log2")] <- segments[i,c("cn", "log2")] + tbl[as.numeric(names(i)),c("cn", "log2")] <- segments[i,c("C", "seg.mean")] tbl } diff --git a/snappy_wrappers/wrappers/cbioportal/generate_cna/wrapper.py b/snappy_wrappers/wrappers/cbioportal/generate_cna/wrapper.py index a26b42146..12e073efd 100644 --- a/snappy_wrappers/wrappers/cbioportal/generate_cna/wrapper.py +++ b/snappy_wrappers/wrappers/cbioportal/generate_cna/wrapper.py @@ -44,7 +44,7 @@ source("{helper_functions}") source("{r_script}") write.table( - cns_to_cna("{snakemake.input}", "{snakemake.params[features]}", "{snakemake.params[pipeline_id]}"), + cns_to_cna("{snakemake.input}", "{snakemake.config[static_data_config][features][path]}", "{snakemake.params[pipeline_id]}"), file="{snakemake.output}", sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE ) __EOF diff --git a/snappy_wrappers/wrappers/cbioportal/helper_functions.R b/snappy_wrappers/wrappers/cbioportal/helper_functions.R index 4162dcfb8..f8efb6a26 100644 --- a/snappy_wrappers/wrappers/cbioportal/helper_functions.R +++ b/snappy_wrappers/wrappers/cbioportal/helper_functions.R @@ -186,10 +186,9 @@ get_id_mappings <- function(org_obj, verbose=FALSE) { if (file.exists(org_obj)) { if (verbose) cat("Gene id mappings taken from file ", org_obj) id_mappings <- read.table(org_obj, sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE, quote="", comment="") - if (all(c("hgnc_symbol", "ensembl_canonical_gene", "entrez_gene_id") %in% colnames(id_mappings))) + if (all(c("symbol", "ensembl_gene_id", "entrez_id") %in% colnames(id_mappings))) id_mappings <- id_mappings |> - dplyr::select(ENSEMBL=ensembl_canonical_gene, SYMBOL=hgnc_symbol, ENTREZ_ID=entrez_gene_id) - stopifnot(all(c("ENSEMBL", "SYMBOL", "ENTREZ_ID") %in% colnames(id_mappings))) + dplyr::select(ENSEMBL=ensembl_gene_id, SYMBOL=symbol, ENTREZ_ID=entrez_id) id_mappings <- id_mappings[,c("ENSEMBL", "SYMBOL", "ENTREZ_ID")] } else { if (grepl("::", org_obj)) { @@ -203,6 +202,7 @@ get_id_mappings <- function(org_obj, verbose=FALSE) { ) } } + stopifnot(all(c("ENSEMBL", "SYMBOL", "ENTREZ_ID") %in% colnames(id_mappings))) id_mappings <- id_mappings |> dplyr::select(ENSEMBL, SYMBOL, ENTREZ_ID) |> dplyr::mutate(ENTREZ_ID=as.character(ENTREZ_ID)) |> diff --git a/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R b/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R index a48a5a848..546d9f1da 100644 --- a/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R +++ b/snappy_wrappers/wrappers/cbioportal/merge_tables/script.R @@ -99,19 +99,14 @@ merge_segments <- function(fns) { if (is.null(names(fns))) stop("Missing sample names") - col_names <- c("chromosome"="chrom", "start"="loc.start", "end"="loc.end", "probes"="num.mark", "log2"="seg.mean") + col_names <- c("chrom", "loc.start", "loc.end", "num.marks", "seg.mean") tbl <- NULL for (sample_id in names(fns)) { cat("Loading", fns[sample_id], "for sample", sample_id, "\n") tmp <- read.table(fns[sample_id], sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE) - if (!all(col_names %in% colnames(tmp))) { - i <- match(names(col_names), colnames(tmp)) - if (any(!is.na(i))) colnames(tmp)[i[!is.na(i)]] <- col_names[!is.na(i)] - } - stopifnot(all(names(col_names) %in% colnames(tmp))) - tmp <- tmp[,names(col_names)] - colnames(tmp) <- col_names - tmp <- cbind(ID=rep(sample_id, nrow(tmp)), tmp) + stopifnot(all(col_names %in% colnames(tmp))) + tmp <- tmp[,col_names] + tmp$ID <- sample_id tbl <- rbind(tbl, tmp) } diff --git a/snappy_wrappers/wrappers/cbioportal/merge_tables/wrapper.py b/snappy_wrappers/wrappers/cbioportal/merge_tables/wrapper.py index b4e4d94b1..d71ffcfdb 100644 --- a/snappy_wrappers/wrappers/cbioportal/merge_tables/wrapper.py +++ b/snappy_wrappers/wrappers/cbioportal/merge_tables/wrapper.py @@ -11,9 +11,12 @@ helper_functions = os.path.join(os.path.dirname(r_script), "..", "helper_functions.R") filenames = ", ".join(['"{}"="{}"'.format(str(k), str(v)) for k, v in snakemake.input.items()]) -extra_args = ", ".join( - ['"{}"="{}"'.format(str(k), str(v)) for k, v in snakemake.params["extra_args"].items()] -) +if "extra_args" in snakemake.params.keys(): + extra_args = ", ".join( + ['"{}"="{}"'.format(str(k), str(v)) for k, v in snakemake.params["extra_args"].items()] + ) +else: + extra_args = "" step = snakemake.config["pipeline_step"]["name"] config = snakemake.config["step_config"][step] diff --git a/snappy_wrappers/wrappers/cnvkit/export/wrapper.py b/snappy_wrappers/wrappers/cnvkit/export/wrapper.py index 38b513d12..0c7af53bb 100644 --- a/snappy_wrappers/wrappers/cnvkit/export/wrapper.py +++ b/snappy_wrappers/wrappers/cnvkit/export/wrapper.py @@ -30,22 +30,25 @@ export TMPDIR=$(mktemp -d) -cnvkit.py export bed {snakemake.input} -o {snakemake.output.bed} +cnvkit.py export bed {snakemake.input} -o $TMPDIR/out.bed +bgzip -c $TMPDIR/out.bed > {snakemake.output.bed} +tabix -f {snakemake.output.bed} + cnvkit.py export seg {snakemake.input} -o {snakemake.output.seg} cnvkit.py export vcf {snakemake.input} -o $TMPDIR/out.vcf - bgzip -c $TMPDIR/out.vcf > {snakemake.output.vcf} tabix -f {snakemake.output.vcf} rm -rf $TMPDIR -d=$(dirname "{snakemake.output.bed}") +d=$(dirname "{snakemake.output.seg}") pushd $d -fn=$(basename "{snakemake.output.bed}") -md5sum $fn > $fn.md5 fn=$(basename "{snakemake.output.seg}") md5sum $fn > $fn.md5 +fn=$(basename "{snakemake.output.bed}") +md5sum $fn > $fn.md5 +md5sum $fn.tbi > $fn.tbi.md5 fn=$(basename "{snakemake.output.vcf}") md5sum $fn > $fn.md5 md5sum $fn.tbi > $fn.tbi.md5 diff --git a/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py b/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py index 2b35d730d..2bf606f6c 100644 --- a/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py +++ b/snappy_wrappers/wrappers/cnvkit/postprocess/wrapper.py @@ -30,11 +30,9 @@ # ----------------------------------------------------------------------------- -uncompressed=$(echo "{snakemake.output.final}" | sed -e "s/\.gz$//") - cat << _EOF | R --vanilla --slave segments <- read.table("{snakemake.input.segment}", sep="\t", header=1, stringsAsFactors=FALSE) -stopifnot(all(c("chromosome", "start", "end") %in% colnames(segments))) +stopifnot(all(c("chromosome", "start", "end", "log2", "probes") %in% colnames(segments))) calls <- read.table("{snakemake.input.call}", sep="\t", header=1, stringsAsFactors=FALSE) stopifnot(all(c("chromosome", "start", "end", "cn") %in% colnames(calls))) @@ -65,24 +63,22 @@ segments[,"start"] <- segments[["start"]]-1 segments[,"end"] <- segments[["end"]]+1 -# Create bed file (abusing name, score & strand to make it bed-6 compatible) -segments[,"start"] <- segments[["start"]]-1 # Bed files are 0-based, semi-open intervals -segments[,"name"] <- sprintf("seg_%d_cn_%d", 1:nrow(segments), segments[["cn"]]) -segments[,"score"] <- pmin(1000, abs(segments[["log2"]])) -segments[,"strand"] <- "+" -segments[segments[["log2"]]<0,"strand"] <- "-" +# Add library name +segments[,"ID"] <- "{snakemake.wildcards[library_name]}" -write.table(segments[,c("chromosome", "start", "end", "name", "score", "strand")], file="$uncompressed", sep="\t", col.names=FALSE, row.names=FALSE, quote=FALSE) -_EOF +# Rename columns to follow DNAcopy format (as implemented in PureCN) +dna_copy_columns <- c(ID="ID", chromosome="chrom", start="loc.start", end="loc.end", probes="num.marks", log2="seg.mean", cn="C") +segments <- segments[,colnames(segments) %in% names(dna_copy_columns)] +colnames(segments) <- dna_copy_columns[colnames(segments)] +segments <- segments[,dna_copy_columns] -bgzip $uncompressed -tabix {snakemake.output.final} +write.table(segments, file="{snakemake.output.final}", sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE) +_EOF d=$(dirname "{snakemake.output.final}") pushd $d fn=$(basename "{snakemake.output.final}") md5sum $fn > $fn.md5 -md5sum $fn.tbi > $fn.tbi.md5 popd """ ) diff --git a/snappy_wrappers/wrappers/dkfz_bias_filter/environment.yaml b/snappy_wrappers/wrappers/dkfz_bias_filter/environment.yaml index bfa788b65..ef3fe295f 100644 --- a/snappy_wrappers/wrappers/dkfz_bias_filter/environment.yaml +++ b/snappy_wrappers/wrappers/dkfz_bias_filter/environment.yaml @@ -2,5 +2,7 @@ channels: - conda-forge - bioconda dependencies: +- htslib ==1.3.1 - dkfz-bias-filter ==1.2.3a -- bcftools +# bcftools incompatible with dkfz-bias-filter in bioconda (2023-10-13) +# - bcftools diff --git a/snappy_wrappers/wrappers/dkfz_bias_filter/wrapper.py b/snappy_wrappers/wrappers/dkfz_bias_filter/wrapper.py index 930ecd2a6..08c0bd829 100644 --- a/snappy_wrappers/wrappers/dkfz_bias_filter/wrapper.py +++ b/snappy_wrappers/wrappers/dkfz_bias_filter/wrapper.py @@ -44,7 +44,9 @@ {snakemake.config[static_data_config][reference][path]} \ ${{out%.gz}} +# bcftools incompatible with dkfzbiasfilter.py in bioconda (2023-10-13) if [[ ! -s ${{out%.gz}} ]]; then + # zgrep '^#' {snakemake.input.vcf} \ bcftools view --header-only {snakemake.input.vcf} \ > ${{out%.gz}} fi diff --git a/snappy_wrappers/wrappers/eb_filter/wrapper.py b/snappy_wrappers/wrappers/eb_filter/wrapper.py index 910c5b70d..821477ec8 100644 --- a/snappy_wrappers/wrappers/eb_filter/wrapper.py +++ b/snappy_wrappers/wrappers/eb_filter/wrapper.py @@ -40,7 +40,20 @@ # Used to be: # filter='FILTER == "germline_risk" || FILTER == "t_lod_fstar" || FILTER == "OffExome" || ANN ~ "stream_gene_variant"' if [[ {snakemake.input.vcf} == *"mutect2"* ]]; then - filter='FILTER == "germline" || FILTER == "weak_evidence" || FILTER == "OffExome" || ANN ~ "stream_gene_variant"' + filter="" + for f in $(echo "germline weak_evidence OffExome" | tr ' ' '\n') + do + use="Yes" + zgrep -q "^##FILTER= $TMPDIR/tmp.vcf.gz +mv $TMPDIR/tmp.vcf.gz {snakemake.output.vcf} tabix -f {snakemake.output.vcf} pushd $(dirname {snakemake.output.vcf}) && \ diff --git a/snappy_wrappers/wrappers/mutect2_par/run/parallel_mutect2.py b/snappy_wrappers/wrappers/mutect2_par/run/parallel_mutect2.py index d2713eaa1..9de25ac92 100644 --- a/snappy_wrappers/wrappers/mutect2_par/run/parallel_mutect2.py +++ b/snappy_wrappers/wrappers/mutect2_par/run/parallel_mutect2.py @@ -33,7 +33,7 @@ def __init__(self, snakemake): self.job_resources = ResourceUsage( threads=1, memory=gib_to_string(14.0 * self.get_job_mult_memory()), - time=hours(1 * self.get_job_mult_time()), + time=hours(4 * self.get_job_mult_time()), partition=os.getenv("SNAPPY_PIPELINE_PARTITION"), ) self.merge_resources = ResourceUsage( diff --git a/snappy_wrappers/wrappers/purecn/coverage/wrapper.py b/snappy_wrappers/wrappers/purecn/coverage/wrapper.py index 20ae81288..0691d31ee 100644 --- a/snappy_wrappers/wrappers/purecn/coverage/wrapper.py +++ b/snappy_wrappers/wrappers/purecn/coverage/wrapper.py @@ -86,6 +86,15 @@ mkdir -p $(dirname {snakemake.output.coverage}) apptainer exec --home $PWD {bindings} {container} $cmd +# Rename coverage file name +d=$(dirname {snakemake.output.coverage}) +mapper="{snakemake.wildcards[mapper]}" +libname="{snakemake.wildcards[library_name]}" +fn="$d/$mapper.${{libname}}_coverage_loess.txt.gz" + +test -e $fn +mv $fn {snakemake.output.coverage} + pushd $(dirname {snakemake.output.coverage}) md5sum $(basename {snakemake.output.coverage}) > $(basename {snakemake.output.coverage}).md5 popd diff --git a/snappy_wrappers/wrappers/purecn/create_panel/wrapper.py b/snappy_wrappers/wrappers/purecn/create_panel/wrapper.py index 9ee6f63d4..5224d6084 100644 --- a/snappy_wrappers/wrappers/purecn/create_panel/wrapper.py +++ b/snappy_wrappers/wrappers/purecn/create_panel/wrapper.py @@ -12,8 +12,8 @@ step = snakemake.config["pipeline_step"]["name"] config = snakemake.config["step_config"][step]["purecn"] -if "genomicsDB" in config.keys() and config["genomicsDB"]: - genomicsDB = config["genomicsDB"] +if "path_genomicsDB" in config.keys() and config["path_genomicsDB"]: + genomicsDB = config["path_genomicsDB"] else: genomicsDB = "" diff --git a/snappy_wrappers/wrappers/purecn/run/wrapper.py b/snappy_wrappers/wrappers/purecn/run/wrapper.py index 0db05d037..a939f333f 100644 --- a/snappy_wrappers/wrappers/purecn/run/wrapper.py +++ b/snappy_wrappers/wrappers/purecn/run/wrapper.py @@ -93,11 +93,22 @@ echo "$checksum" }} +# Rename PureCN files to snappy conventions +rename() {{ + to=$1 + d=$(dirname $to) + f=$(basename $to) + echo $f | grep -q "^{snakemake.wildcards[mapper]}.purecn.{snakemake.wildcards[library_name]}" + from=$(echo $f | sed -e "s/^{snakemake.wildcards[mapper]}.purecn.//") + test -e $d/$from + mv $d/$from $to +}} + outdir=$(dirname {snakemake.output.segments}) mkdir -p $outdir # Run PureCN with a panel of normals -cmd="/usr/local/bin/Rscript PureCN.R \ +cmd="/usr/local/bin/Rscript /opt/PureCN/PureCN.R \ --sampleid {snakemake.wildcards[library_name]} \ --tumor {snakemake.input.tumor} \ --vcf {bound_files[vcf]} \ @@ -106,11 +117,42 @@ --intervals {bound_files[intervals]} \ --genome {config[genome_name]} \ --out $outdir --out-vcf --force \ - --seed {config[seed]} --parallel --cores={snakemake.threads} \ + --seed {config[seed]} --parallel --cores {snakemake.threads} \ {extra_commands} " apptainer exec --home $PWD {bindings} {config[path_container]} $cmd +rename {snakemake.output.segments} +rename {snakemake.output.ploidy} +rename {snakemake.output.pvalues} +rename {snakemake.output.vcf} +rename {snakemake.output.vcf_tbi} +rename {snakemake.output.loh} + +# Fix chromosome names (https://github.com/lima1/PureCN/issues/331) +seg_chrnames=$(tail -n +2 {snakemake.output.segments} | cut -f 2 | sort | uniq) +vcf_chrnames=$(zgrep '^##contig= {snakemake.output.segments_md5} md5 {snakemake.output.ploidy} > {snakemake.output.ploidy_md5} md5 {snakemake.output.pvalues} > {snakemake.output.pvalues_md5} diff --git a/snappy_wrappers/wrappers/scarHRD/environment.yaml b/snappy_wrappers/wrappers/scarHRD/environment.yaml index a86405d52..9093fa7cb 100644 --- a/snappy_wrappers/wrappers/scarHRD/environment.yaml +++ b/snappy_wrappers/wrappers/scarHRD/environment.yaml @@ -4,3 +4,16 @@ channels: dependencies: - python =3.9 - r-base + - r-remotes + # scarHRD requirements (+sequenza) + - r-data.table + # sequenza requirements (+copynumber) + - r-pbapply + - r-squash + - r-iotools + - r-readr + - r-seqminer + # copynumber requirements + - bioconductor-S4Vectors + - bioconductor-IRanges + - bioconductor-GenomicRanges diff --git a/snappy_wrappers/wrappers/scarHRD/install/environment.yaml b/snappy_wrappers/wrappers/scarHRD/install/environment.yaml new file mode 120000 index 000000000..2e107ac86 --- /dev/null +++ b/snappy_wrappers/wrappers/scarHRD/install/environment.yaml @@ -0,0 +1 @@ +../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/scarHRD/install/wrapper.py b/snappy_wrappers/wrappers/scarHRD/install/wrapper.py new file mode 100644 index 000000000..ca4d0d9bd --- /dev/null +++ b/snappy_wrappers/wrappers/scarHRD/install/wrapper.py @@ -0,0 +1,22 @@ +# -*- coding: utf-8 -*- +"""Installation of scarHRD non-standard packages""" + +import os +from pathlib import Path +import sys + +# The following is required for being able to import snappy_wrappers modules +# inside wrappers. These run in an "inner" snakemake process which uses its +# own conda environment which cannot see the snappy_pipeline installation. +base_dir = os.path.normpath(os.path.join(os.path.dirname(__file__), "..", "..", "..", "..")) +sys.path.insert(0, base_dir) + +from snappy_wrappers.utils import install_R_package # noqa: E402 + +__author__ = "Eric Blanc " + +dest = os.path.dirname(str(snakemake.output.done)) +for package in snakemake.params.packages: + install_R_package(dest, package["name"], package["repo"]) + +Path(str(snakemake.output.done)).touch() diff --git a/snappy_wrappers/wrappers/scarHRD/run/wrapper.py b/snappy_wrappers/wrappers/scarHRD/run/wrapper.py index 7e1261fa5..c825f46f1 100644 --- a/snappy_wrappers/wrappers/scarHRD/run/wrapper.py +++ b/snappy_wrappers/wrappers/scarHRD/run/wrapper.py @@ -7,7 +7,7 @@ __author__ = "Eric Blanc " -lib_path = os.path.dirname(snakemake.input.done) +lib_path = os.path.realpath(os.path.dirname(snakemake.input.done)) step = snakemake.config["pipeline_step"]["name"] genome = snakemake.config["static_data_config"]["reference"]["path"] @@ -49,23 +49,30 @@ export R_LIBS_USER="{lib_path}" export VROOM_CONNECTION_SIZE=2000000000 -export R_LIBS_PATH="{lib_path}" -export VROOM_CONNECTION_SIZE=2000000000 +# Necessary because scarHRD litters the current directory +pushd $(dirname {snakemake.output.scarHRD}) + +fn=$(basename "{snakemake.output.scarHRD}") cat << __EOF | R --vanilla --slave library("scarHRD") -tbl <- scar_score("{snakemake.input.seqz}", reference="{genome_name}", seqz=TRUE, chr.in.name={chr_in_name}, outputdir=dirname("{snakemake.output.scarHRD}")) -cat('{{\n', file="{snakemake.output.scarHRD}") -cat(' "HRD": ', tbl[1,1], ',\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) -cat(' "Telomeric AI": ', tbl[1,2], ',\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) -cat(' "LST": ', tbl[1,3], ',\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) -cat(' "HRD-sum": ', tbl[1,4], '\n', sep="", file="{snakemake.output.scarHRD}", append=TRUE) -cat('}}\n', file="{snakemake.output.scarHRD}", append=TRUE) +tbl <- scar_score("{snakemake.input.seqz}", reference="{genome_name}", seqz=TRUE, chr.in.name={chr_in_name}) + +warnings() + +cat('{{\n', file="$fn") +cat(' "HRD": ', tbl[1,1], ',\n', sep="", file="$fn", append=TRUE) +cat(' "Telomeric AI": ', tbl[1,2], ',\n', sep="", file="$fn", append=TRUE) +cat(' "LST": ', tbl[1,3], ',\n', sep="", file="$fn", append=TRUE) +cat(' "HRD-sum": ', tbl[1,4], '\n', sep="", file="$fn", append=TRUE) +cat('}}\n', file="$fn", append=TRUE) __EOF -pushd $(dirname {snakemake.output.scarHRD}) ; f=$(basename {snakemake.output.scarHRD}) ; md5sum $f > $f.md5 ; popd +md5sum $fn > $fn.md5 + +popd """ ) diff --git a/snappy_wrappers/wrappers/sequenza/coverage/environment.yaml b/snappy_wrappers/wrappers/sequenza/coverage/environment.yaml new file mode 120000 index 000000000..050fd4ee3 --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/coverage/environment.yaml @@ -0,0 +1 @@ +../gcreference/environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/sequenza/coverage/wrapper.py b/snappy_wrappers/wrappers/sequenza/coverage/wrapper.py new file mode 100644 index 000000000..cc524a261 --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/coverage/wrapper.py @@ -0,0 +1,72 @@ +"""CUBI+Snakemake wrapper code for sequenza (sequenza-utils, pileups) +""" + +import os +import sys + +# The following is required for being able to import snappy_wrappers modules +# inside wrappers. These run in an "inner" snakemake process which uses its +# own conda environment which cannot see the snappy_pipeline installation. +base_dir = os.path.normpath(os.path.join(os.path.dirname(__file__), "..", "..", "..", "..")) +sys.path.insert(0, base_dir) + +from snakemake import shell + +from snappy_wrappers.tools.genome_windows import yield_contigs + +__author__ = "Eric Blanc " + + +step = snakemake.config["pipeline_step"]["name"] +config = snakemake.config["step_config"][step]["sequenza"] +genome = snakemake.config["static_data_config"]["reference"]["path"] +length = config["length"] + +f = open(genome + ".fai", "rt") +contigs = " ".join(yield_contigs(f, config.get("ignore_chroms"))) +f.close() + +extra_arguments = " ".join( + ["--{} {}".format(k, v) for k, v in config.get("extra_arguments", {}).items()] +) + +shell.executable("/bin/bash") + +shell( + r""" +set -x + +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} + +# Also pipe stderr to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi + +sequenza-utils bam2seqz \ + -gc {snakemake.input.gc} --fasta {genome} \ + -n {snakemake.input.normal_bam} --tumor {snakemake.input.tumor_bam} \ + -C {contigs} {extra_arguments} \ + | sequenza-utils seqz_binning -s - \ + -w {length} -o {snakemake.output.seqz} + +pushd $(dirname {snakemake.output.seqz}) ; f=$(basename {snakemake.output.seqz}) ; md5sum $f > $f.md5 ; popd +""" +) + +# Compute MD5 sums of logs. +shell( + r""" +md5sum {snakemake.log.log} >{snakemake.log.log_md5} +""" +) diff --git a/snappy_wrappers/wrappers/sequenza/environment.yaml b/snappy_wrappers/wrappers/sequenza/environment.yaml deleted file mode 100644 index b6a8c8b49..000000000 --- a/snappy_wrappers/wrappers/sequenza/environment.yaml +++ /dev/null @@ -1,10 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - python =3.9 - - sequenza-utils - - r-sequenza - - r-devtools - - r-data.table - - samtools diff --git a/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml b/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml deleted file mode 120000 index 2e107ac86..000000000 --- a/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml +++ /dev/null @@ -1 +0,0 @@ -../environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml b/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml new file mode 100644 index 000000000..72d44247a --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - python =3.9 + - sequenza-utils + - samtools diff --git a/snappy_wrappers/wrappers/sequenza/install/environment.yaml b/snappy_wrappers/wrappers/sequenza/install/environment.yaml new file mode 100644 index 000000000..dc180c107 --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/install/environment.yaml @@ -0,0 +1,18 @@ +channels: + - conda-forge + - bioconda +dependencies: + - python =3.9 + - r-base + - r-remotes + # sequenza requirements (+copynumber) + - r-pbapply + - r-squash + - r-iotools + - r-readr + - r-seqminer + - r-data.table + # copynumber requirements + - bioconductor-S4Vectors + - bioconductor-IRanges + - bioconductor-GenomicRanges diff --git a/snappy_wrappers/wrappers/sequenza/install/wrapper.py b/snappy_wrappers/wrappers/sequenza/install/wrapper.py new file mode 100644 index 000000000..780a8347f --- /dev/null +++ b/snappy_wrappers/wrappers/sequenza/install/wrapper.py @@ -0,0 +1,22 @@ +# -*- coding: utf-8 -*- +"""Installation of sequenza non-standard packages""" + +import os +from pathlib import Path +import sys + +# The following is required for being able to import snappy_wrappers modules +# inside wrappers. These run in an "inner" snakemake process which uses its +# own conda environment which cannot see the snappy_pipeline installation. +base_dir = os.path.normpath(os.path.join(os.path.dirname(__file__), "..", "..", "..", "..")) +sys.path.insert(0, base_dir) + +from snappy_wrappers.utils import install_R_package # noqa: E402 + +__author__ = "Eric Blanc " + +dest = os.path.dirname(str(snakemake.output.done)) +for package in snakemake.params.packages: + install_R_package(dest, package["name"], package["repo"]) + +Path(str(snakemake.output.done)).touch() diff --git a/snappy_wrappers/wrappers/sequenza/report/wrapper.py b/snappy_wrappers/wrappers/sequenza/report/wrapper.py index 28c1b18a6..3db1e1ec6 100644 --- a/snappy_wrappers/wrappers/sequenza/report/wrapper.py +++ b/snappy_wrappers/wrappers/sequenza/report/wrapper.py @@ -68,6 +68,7 @@ def config_to_r(x): fi export R_LIBS_USER=$(dirname {snakemake.input.packages}) +export VROOM_CONNECTION_SIZE=2000000000 R --vanilla --slave << __EOF library(sequenza) @@ -80,11 +81,11 @@ def config_to_r(x): args <- c(args, {args_fit}) CP <- do.call(sequenza.fit, args=args) -sequenza.results(sequenza.extract=seqz, cp.table=CP, sample.id="{snakemake.params[sample_id]}", out.dir=dirname("{snakemake.output.done}")) +sequenza.results(sequenza.extract=seqz, cp.table=CP, sample.id="{snakemake.wildcards[library_name]}", out.dir=dirname("{snakemake.output.done}")) __EOF -pushd $(dirname {snakemake.output.done}) ; for f in $(ls) ; do md5sum $f > $f.md5 ; done ; popd +pushd $(dirname {snakemake.output.done}) ; fns=$(ls) ; for f in $fns ; do md5sum $f > $f.md5 ; done ; popd touch {snakemake.output.done} """ diff --git a/snappy_wrappers/wrappers/sequenza/run/environment.yaml b/snappy_wrappers/wrappers/sequenza/run/environment.yaml index 2e107ac86..04535f055 120000 --- a/snappy_wrappers/wrappers/sequenza/run/environment.yaml +++ b/snappy_wrappers/wrappers/sequenza/run/environment.yaml @@ -1 +1 @@ -../environment.yaml \ No newline at end of file +../install/environment.yaml \ No newline at end of file diff --git a/snappy_wrappers/wrappers/sequenza/run/wrapper.py b/snappy_wrappers/wrappers/sequenza/run/wrapper.py index 13fa1f64d..c768d3937 100644 --- a/snappy_wrappers/wrappers/sequenza/run/wrapper.py +++ b/snappy_wrappers/wrappers/sequenza/run/wrapper.py @@ -1,4 +1,4 @@ -"""CUBI+Snakemake wrapper code for sequenza (sequenza-utils, pileups) +"""CUBI+Snakemake wrapper code for sequenza (coverage analysis in R) """ import os @@ -16,18 +16,35 @@ __author__ = "Eric Blanc " + +def config_to_r(x): + if x is None: + return "NULL" + if isinstance(x, str): + return f'"{x}"' + if isinstance(x, bool): + return "TRUE" if x else "FALSE" + if isinstance(x, list): + # TODO: verify that all elements are either bool, str or numeric + return "c({})".format(", ".join([config_to_r(xx) for xx in x])) + if isinstance(x, dict): + return "list({})".format( + ", ".join(['"{}"={}'.format(k, config_to_r(v)) for k, v in x.items()]) + ) + return str(x) + + step = snakemake.config["pipeline_step"]["name"] config = snakemake.config["step_config"][step]["sequenza"] genome = snakemake.config["static_data_config"]["reference"]["path"] length = config["length"] f = open(genome + ".fai", "rt") -contigs = " ".join(yield_contigs(f, config.get("ignore_chroms"))) +contigs = config_to_r(list(yield_contigs(f, config.get("ignore_chroms")))) f.close() -extra_arguments = " ".join( - ["--{} {}".format(k, v) for k, v in config.get("extra_arguments", {}).items()] -) +args_extract = config_to_r(dict(config["extra_args_extract"])) +args_fit = config_to_r(dict(config["extra_args_fit"])) shell.executable("/bin/bash") @@ -52,14 +69,52 @@ fi fi -sequenza-utils bam2seqz \ - -gc {snakemake.input.gc} --fasta {genome} \ - -n {snakemake.input.normal_bam} --tumor {snakemake.input.tumor_bam} \ - -C {contigs} {extra_arguments} \ - | sequenza-utils seqz_binning -s - \ - -w {length} -o {snakemake.output.seqz} +export R_LIBS_USER=$(dirname {snakemake.input.packages}) +export VROOM_CONNECTION_SIZE=2000000000 + +R --vanilla --slave << __EOF +library(sequenza) + +# Follow sequenza documentation https://bitbucket.org/sequenzatools/sequenza/src/master/ +args <- list(file="{snakemake.input.seqz}", assembly="{config[assembly]}", chromosome.list={contigs}) +args <- c(args, {args_extract}) +seqz <- do.call(sequenza.extract, args=args) + +args <- list(sequenza.extract=seqz, chromosome.list={contigs}, mc.cores=1) +args <- c(args, {args_fit}) +CP <- do.call(sequenza.fit, args=args) + +sequenza.results(sequenza.extract=seqz, cp.table=CP, sample.id="{snakemake.wildcards[library_name]}", out.dir=dirname("{snakemake.output.done}")) + +warnings() + +# Convert *_segment.txt to *_dnacopy.seg to follow pipeline output format +segments <- file.path(dirname("{snakemake.output.done}"), sprintf("%s_segments.txt", "{snakemake.wildcards[library_name]}")) +stopifnot(file.exists(segments)) +dnacopy <- read.table(segments, sep="\t", header=1, stringsAsFactors=FALSE, check.names=FALSE) + +dnacopy[,"ID"] <- "{snakemake.wildcards[library_name]}" +dnacopy[,"depth.ratio"] <- log2(dnacopy[,"depth.ratio"]) + +col_names <- c( + "ID"="ID", + "chromosome"="chrom", + "start.pos"="loc.start", + "end.pos"="loc.end", + "N.BAF"="num.mark", + "depth.ratio"="seg.mean", + "CNt"="C" +) +stopifnot(all(names(col_names) %in% colnames(dnacopy))) +dnacopy <- dnacopy[,names(col_names)] +colnames(dnacopy) <- col_names + +write.table(dnacopy, file="{snakemake.output.seg}", sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE) +__EOF -pushd $(dirname {snakemake.output.seqz}) ; f=$(basename {snakemake.output.seqz}) ; md5sum $f > $f.md5 ; popd +pushd $(dirname {snakemake.output.seg}) ; f=$(basename {snakemake.output.seg}) ; md5sum $f > $f.md5 ; popd +pushd $(dirname {snakemake.output.done}) ; fns=$(ls) ; for f in $fns ; do md5sum $f > $f.md5 ; done ; popd +touch {snakemake.output.done} """ ) diff --git a/snappy_wrappers/wrappers/somatic_cnv_checking/cnv-check-plot.R b/snappy_wrappers/wrappers/somatic_cnv_checking/cnv-check-plot.R index f6d54977e..3845e2e0a 100644 --- a/snappy_wrappers/wrappers/somatic_cnv_checking/cnv-check-plot.R +++ b/snappy_wrappers/wrappers/somatic_cnv_checking/cnv-check-plot.R @@ -13,7 +13,7 @@ vcf_to_table <- function(vcf, sample, amplification=7) { stopifnot(all(lengths(VariantAnnotation::alt(vcf)) == 2)) x <- data.frame( - CHROM=GenomicRanges::seqnames(SummarizedExperiment::rowRanges(vcf)), + CHROM=as.character(GenomicRanges::seqnames(SummarizedExperiment::rowRanges(vcf))), POS=GenomicRanges::start(SummarizedExperiment::rowRanges(vcf)), REF=VariantAnnotation::ref(vcf), ALT=unlist(lapply(VariantAnnotation::alt(vcf), function(a) a[1])), @@ -34,7 +34,8 @@ cnv_to_table <- function(cnv) { colnames(y) <- c("CHROM", "start", "stop", "name", "LFC", "strand") y <- y |> dplyr::mutate(LFC=replace(LFC, strand == "-", -abs(LFC[strand=="-"]))) |> - dplyr::mutate(start=start + 1) + dplyr::mutate(start=start + 1) |> + dplyr::mutate(CHROM=as.character(CHROM)) y } diff --git a/snappy_wrappers/wrappers/somatic_cnv_checking/wrapper.py b/snappy_wrappers/wrappers/somatic_cnv_checking/wrapper.py index 924c194e0..bf1277484 100644 --- a/snappy_wrappers/wrappers/somatic_cnv_checking/wrapper.py +++ b/snappy_wrappers/wrappers/somatic_cnv_checking/wrapper.py @@ -58,7 +58,7 @@ y <- read.table("{snakemake.input.tsv}", sep="\t", header=1, check.names=FALSE) y <- y |> dplyr::mutate(Call=cn_to_call(CN)) -y <- y |> dplyr::left_join(genome_lengths, by="CHROM") |> dplyr::mutate(from=start + Offset, to=stop + Offset) +y <- y |> dplyr::mutate(CHROM=as.character(CHROM)) |> dplyr::left_join(genome_lengths, by="CHROM") |> dplyr::mutate(from=start + Offset, to=stop + Offset) pdf("{snakemake.output.cnv}", height=6.22, width=9.33) plot_cnv(x, scale="log2") + ggplot2::ggtitle("{snakemake.wildcards[library_name]}") diff --git a/snappy_wrappers/wrappers/star/wrapper.py b/snappy_wrappers/wrappers/star/wrapper.py index db1f277f6..ead553e6e 100644 --- a/snappy_wrappers/wrappers/star/wrapper.py +++ b/snappy_wrappers/wrappers/star/wrapper.py @@ -139,7 +139,7 @@ fi quant_mode="" - if [[ -n "{snakemake.config[step_config][ngs_mapping][star][path_features]}" ]] + if [[ -n "{snakemake.config[static_data_config][features][path]}" ]] then quant_mode="$quant_mode GeneCounts" fi @@ -175,8 +175,8 @@ $(if [[ -n "$quant_mode" ]]; then \ echo "--quantMode $quant_mode" fi) \ - $(if [[ -n "{snakemake.config[step_config][ngs_mapping][star][path_features]}" ]]; then \ - echo --sjdbGTFfile "{snakemake.config[step_config][ngs_mapping][star][path_features]}" + $(if [[ -n "{snakemake.config[static_data_config][features][path]}" ]]; then \ + echo --sjdbGTFfile "{snakemake.config[static_data_config][features][path]}" fi) \ $(if [[ "{snakemake.config[step_config][ngs_mapping][star][mask_duplicates]}" == "True" ]]; then \ echo " --outStd SAM " ; \ @@ -200,12 +200,10 @@ index_bam {snakemake.output.bam} -# Optional output: gene counts & mapping on transcriptome ----------------------------------------- +mv $TMPDIR/pre.d/out.ReadsPerGene.out.tab {out_gc} +compute-md5 {out_gc} {out_gc}.md5 -if [[ -n "{snakemake.config[step_config][ngs_mapping][star][path_features]}" ]]; then - mv $TMPDIR/pre.d/out.ReadsPerGene.out.tab {out_gc} - compute-md5 {out_gc} {out_gc}.md5 -fi +# Optional output: mapping on transcriptome ------------------------------------------------------- if [[ "{snakemake.config[step_config][ngs_mapping][star][transcriptome]}" = "True" ]]; then if [[ "{snakemake.config[step_config][ngs_mapping][star][mask_duplicates]}" == "True" ]]; then diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py index 579de04c3..94ab53b00 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/protein_mutation_parser.py @@ -212,7 +212,7 @@ def _build_protein_pattern(): + "(" + "|".join( [ - "(0|=|\?)", # noqa: W605 + "(0\??|=|\?)", # noqa: W605 substitution, # 4: ref, 5: position, 6: alt duplication, # 7: start, 8: start pos, 10: end, 11: end pos deletion, # 12: start, 13: start pos, 15: end, 16: end pos diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py index 620514f32..d97d17b53 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/wrapper.py @@ -12,7 +12,7 @@ vcf_to_table = os.path.join(os.path.dirname(os.path.realpath(__file__)), "vcf_to_table.py") if config["somatic_variant_annotation_tool"] == "vep": vcf_to_table_config = os.path.join(os.path.dirname(os.path.realpath(__file__)), "vep.yaml") -elif config["somatic_variant_annotation_tool"] == "jannovar_annotate_somatic_vcf": +elif config["somatic_variant_annotation_tool"] == "jannovar": vcf_to_table_config = os.path.join(os.path.dirname(os.path.realpath(__file__)), "jannovar.yaml") else: raise Exception( diff --git a/snappy_wrappers/wrappers/vcfpy/add_bed/wrapper.py b/snappy_wrappers/wrappers/vcfpy/add_bed/wrapper.py index d98068a87..4ef49107e 100644 --- a/snappy_wrappers/wrappers/vcfpy/add_bed/wrapper.py +++ b/snappy_wrappers/wrappers/vcfpy/add_bed/wrapper.py @@ -1,146 +1,59 @@ import math -import numbers +import os import re -import subprocess +import shutil +import tempfile from snakemake.shell import shell import tabix import vcfpy -NAME_PATTERN = re.compile("^seg_([0-9]+)_cn_([0-9]+)$") - -LFC = {"ID": "LFC", "Number": 1, "Type": "Float", "Description": "Log2 fold change from coverage"} -CN = { - "ID": "CN", - "Number": 1, - "Type": "Integer", - "Description": "Number of allele called by the CNV caller", -} - step = snakemake.config["pipeline_step"]["name"] config = snakemake.config["step_config"][step] -bed = tabix.open(snakemake.input.cnv) +tempdir = tempfile.mkdtemp() -ps = [] -nProc = 0 -ps += [ - subprocess.Popen( - ["bcftools", "merge", snakemake.input.normal, snakemake.input.tumor], stdout=subprocess.PIPE - ) +variants = [ + f"bcftools merge {snakemake.input.normal} {snakemake.input.tumor}", + 'bcftools filter --include "N_ALT=2 & FORMAT/AD[:2]=0"', ] -nProc += 1 -ps += [ - subprocess.Popen( - ["bcftools", "filter", "--include", "N_ALT=2 & FORMAT/AD[:2]=0"], - stdin=ps[nProc - 1].stdout, - stdout=subprocess.PIPE, - text=True, - ) -] -ps[nProc - 1].stdout.close() # Allow p1 to receive a SIGPIPE if p2 exits. -nProc += 1 if "excluded_regions" in config and config["excluded_regions"]: - ps += [ - subprocess.Popen( - ["bcftools", "view", "--targets-file", "^" + config["excluded_regions"]], - stdin=ps[nProc - 1].stdout, - stdout=subprocess.PIPE, - text=True, - ) - ] - ps[nProc - 1].stdout.close() - nProc += 1 -reader = vcfpy.Reader.from_stream(ps[nProc - 1].stdout) + variants.append(f"bcftools view --targets-file ^{config['excluded_regions']}") +variants = " \\\n | ".join(variants) -sample = snakemake.wildcards["library_name"] -iSample = reader.header.samples.name_to_idx[sample] - -reader.header.add_format_line(LFC) -reader.header.add_format_line(CN) - -writer = vcfpy.Writer.from_path(snakemake.output.vcf, reader.header) - -segments = {} -for variant in reader: - logFoldChange = None - cn = None - - # Add default (missing) values for all samples - variant.add_format("LFC", logFoldChange) - variant.add_format("CN", cn) - - try: - locii = list(bed.query(variant.CHROM, variant.affected_start, variant.affected_end + 1)) - except tabix.TabixError as e: - print( - "Variant {}:{}{}>{} not covered by segmentation of sample {}".format( - variant.CHROM, variant.POS, variant.REF, variant.ALT[0].value, sample - ) - ) - continue - - if len(locii) == 0: - print( - "Variant {}:{}{}>{} not covered by segmentation of sample {}".format( - variant.CHROM, variant.POS, variant.REF, variant.ALT[0].value, sample - ) - ) - elif len(locii) == 1: - for locus in locii: - logFoldChange = float(locus[4]) - if locus[5] == "-": - logFoldChange = -logFoldChange - m = NAME_PATTERN.match(locus[3]) - assert m - cn = int(m.groups()[1]) - else: - print( - "Variant {}:{}{}>{} crosses segments in sample {}".format( - variant.CHROM, variant.POS, variant.REF, variant.ALT[0].value, sample - ) - ) - for locus in locii: - m = NAME_PATTERN.match(locus[3]) - assert m - if cn is None: - cn = int(m.groups()[1]) - else: - if cn != int(m.groups()[1]): - cn = None - break +shell( + r""" +set -x - variant.calls[iSample].data["LFC"] = logFoldChange - variant.calls[iSample].data["CN"] = cn +# Write out information about conda installation. +conda list >{snakemake.log.conda_list} +conda info >{snakemake.log.conda_info} +md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5} +md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5} - writer.write_record(variant) +# Also pipe stderr to log file +if [[ -n "{snakemake.log.log}" ]]; then + if [[ "$(set +e; tty; set -e)" != "" ]]; then + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + exec 2> >(tee -a "{snakemake.log.log}" >&2) + else + rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log}) + echo "No tty, logging disabled" >"{snakemake.log.log}" + fi +fi - if len(locii) == 1: - locus = locii[0] - if locus[3] not in segments: - segments[locus[3]] = { - "logFoldChange": logFoldChange, - "CHROM": locus[0], - "start": locus[1], - "stop": locus[2], - "BAFs": [], - "NoData": 0, - } - depth = variant.call_for_sample[sample].data["AD"] - if len(depth) == 0: - segments[locus[3]]["NoData"] += 1 - else: - if depth[0] is None: - depth[0] = 0 - if depth[1] is None: - depth[1] = 0 - if depth[0] + depth[1] == 0: - segments[locus[3]]["NoData"] += 1 - else: - baf = min(depth[0], depth[1]) / (depth[0] + depth[1]) - segments[locus[3]]["BAFs"] += [baf] +{variants} \ + | bgzip \ + > {tempdir}/variants.vcf.gz +tabix {tempdir}/variants.vcf.gz -writer.close() +tail -n +2 {snakemake.input.cnv} \ + | awk '{{if ($6 < 0) {{sgn="-"; lfc=-$6}} else {{sgn="+"; lfc=$6}}; printf "%s\t%d\t%d\tseg_%d_cn_%d\t%f\t%s\n", $2, $3-1, $4, NR, $7, lfc, sgn}}' \ + | bgzip \ + > {tempdir}/segments.bed.gz +tabix {tempdir}/segments.bed.gz +""" +) # Implmentation of R's quantile function for continuous quantiles. def quantile(x, probs, na_rm=False, method=7): @@ -183,6 +96,116 @@ def quantile(x, probs, na_rm=False, method=7): return qs +# Adds the seg.mean & C (from *_dnacopy.seg file) to the variant vcf +NAME_PATTERN = re.compile("^seg_([0-9]+)_cn_([0-9]+)$") + +LFC = {"ID": "LFC", "Number": 1, "Type": "Float", "Description": "Log2 fold change from coverage"} +CN = { + "ID": "CN", + "Number": 1, + "Type": "Integer", + "Description": "Number of allele called by the CNV caller", +} + +bed = tabix.open(os.path.join(tempdir, "segments.bed.gz")) + +reader = vcfpy.Reader.from_path(os.path.join(tempdir, "variants.vcf.gz")) + +sample = snakemake.wildcards["library_name"] +iSample = reader.header.samples.name_to_idx[sample] + +reader.header.add_format_line(LFC) +reader.header.add_format_line(CN) + +writer = vcfpy.Writer.from_path(snakemake.output.vcf, reader.header) + +segments = {} +with open(snakemake.log.log, "+at") as log: + for variant in reader: + logFoldChange = None + cn = None + + # Add default (missing) values for all samples + variant.add_format("LFC", logFoldChange) + variant.add_format("CN", cn) + + try: + locii = list(bed.query(variant.CHROM, variant.affected_start, variant.affected_end + 1)) + + if len(locii) == 0: + log.write( + "Variant {}:{}{}>{} not covered by segmentation of sample {}\n".format( + variant.CHROM, variant.POS, variant.REF, variant.ALT[0].value, sample + ) + ) + elif len(locii) == 1: + for locus in locii: + logFoldChange = float(locus[4]) + if locus[5] == "-": + logFoldChange = -logFoldChange + m = NAME_PATTERN.match(locus[3]) + assert m + cn = int(m.groups()[1]) + else: + log.write( + "Variant {}:{}{}>{} crosses segments in sample {}\n".format( + variant.CHROM, variant.POS, variant.REF, variant.ALT[0].value, sample + ) + ) + for locus in locii: + m = NAME_PATTERN.match(locus[3]) + assert m + if cn is None: + cn = int(m.groups()[1]) + else: + if cn != int(m.groups()[1]): + cn = None + break + + except tabix.TabixError as e: + log.write( + "Variant {}:{}{}>{} not covered by segmentation of sample {}\n".format( + variant.CHROM, variant.POS, variant.REF, variant.ALT[0].value, sample + ) + ) + locii = None + + variant.calls[iSample].data["LFC"] = logFoldChange + variant.calls[iSample].data["CN"] = cn + + writer.write_record(variant) + + if locii is None or len(locii) != 1: + continue + + locus = locii[0] + if locus[3] not in segments: + segments[locus[3]] = { + "logFoldChange": logFoldChange, + "CHROM": locus[0], + "start": locus[1], + "stop": locus[2], + "BAFs": [], + "NoData": 0, + } + depth = variant.call_for_sample[sample].data["AD"] + if len(depth) == 0: + segments[locus[3]]["NoData"] += 1 + else: + if depth[0] is None: + depth[0] = 0 + if depth[1] is None: + depth[1] = 0 + if depth[0] + depth[1] == 0: + segments[locus[3]]["NoData"] += 1 + else: + baf = min(depth[0], depth[1]) / (depth[0] + depth[1]) + segments[locus[3]]["BAFs"] += [baf] + + writer.close() + +shutil.rmtree(tempdir) + with open(snakemake.output.tsv, "wt") as f: print( "Number\tCHROM\tstart\tstop\tCN\tLFC\tNvariants\tMin\t1st quartile\tMedian\t3rd quartile\tMax\tNoData", diff --git a/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py b/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py index d225952e9..2a41b8c97 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py +++ b/tests/snappy_pipeline/workflows/test_workflows_cbioportal_export.py @@ -23,11 +23,12 @@ def minimal_config(): static_data_config: reference: path: /path/to/ref.fa + features: + path: /path/to/features.gtf step_config: ngs_mapping: star: - path_features: /path/to/gtf cbioportal_export: # Paths to snappy steps containing results to be uploaded path_ngs_mapping: /NGS_MAPPING @@ -417,7 +418,7 @@ def test_cbioportal_mutations_step_part_get_resource_usage(cbioportal_export_wor def test_cbioportal_cns2cna_step_part_get_input_files(cbioportal_export_workflow): """Tests cbioportalCns2CnaStepPart.get_input_files()""" expected = { - "cns": "/COPY_NUMBER/output/{mapper}.{caller}.{tumor_library}/out/{mapper}.{caller}.{tumor_library}.cns" + "DNAcopy": "/COPY_NUMBER/output/{mapper}.{caller}.{tumor_library}/out/{mapper}.{caller}.{tumor_library}_dnacopy.seg" } actual = cbioportal_export_workflow.get_input_files("cbioportal_cns2cna", "run") assert actual == expected @@ -449,7 +450,7 @@ def test_cbioportal_cns2cna_step_part_get_log_file(cbioportal_export_workflow): def test_cbioportal_cns2cna_step_part_get_args(cbioportal_export_workflow): """Tests cbioportalCns2CnaStepPart.get_args()""" expected = { - "features": "/path/to/gtf", + "features": "/path/to/features.gtf", "pipeline_id": "ENSEMBL", } actual = cbioportal_export_workflow.get_args("cbioportal_cns2cna", "run") @@ -567,7 +568,7 @@ def test_cbioportal_segment_step_part_get_input_files(cbioportal_export_workflow """Tests cbioportalSegmentStepPart.get_input_files()""" # Define expected sample = "P00{i}-T{t}" - base_name = "/COPY_NUMBER/output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/out/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.cns" + base_name = "/COPY_NUMBER/output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/out/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1_dnacopy.seg" expected = { sample.format(i=i, t=t): base_name.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2)) } @@ -646,7 +647,7 @@ def test_cbioportal_expression_step_part_get_args(cbioportal_export_workflow): """Tests cbioportalExpressionStepPart.get_args()""" expected = { "action_type": "expression", - "extra_args": {"tx_obj": "/path/to/gtf", "pipeline_id": "ENSEMBL"}, + "extra_args": {"tx_obj": "/path/to/features.gtf", "pipeline_id": "ENSEMBL"}, } actual = cbioportal_export_workflow.get_args("cbioportal_expression", "run") assert actual == expected diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py index 365b5bce4..4dc433ba9 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py +++ b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py @@ -357,6 +357,8 @@ def test_star_step_part_get_output_files(ngs_mapping_workflow): report_base_out = "work/star.{library_name}/report/bam_qc/star.{library_name}" log_base_out = "work/star.{library_name}/log/star.{library_name}" expected = get_expected_output_files_dict(bam_base_out, report_base_out, log_base_out) + expected["gene_counts"] = "work/star.{library_name}/out/star.{library_name}.GeneCounts.tab" + expected["gene_counts_md5"] = expected["gene_counts"] + ".md5" # Get actual actual = ngs_mapping_workflow.get_output_files("star", "run") assert actual == expected diff --git a/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals.py b/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals.py index 7ac498f81..b582f5973 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals.py +++ b/tests/snappy_pipeline/workflows/test_workflows_panel_of_normals.py @@ -532,7 +532,7 @@ def test_purecn_step_part_get_input_files_coverage(panel_of_normals_workflow): wildcards = Wildcards( fromdict={ "mapper": "bwa", - "normal_library": "P001-N1-DNA1-WGS1", + "library_name": "P001-N1-DNA1-WGS1", } ) expected = { @@ -547,7 +547,7 @@ def test_purecn_step_part_get_input_files_coverage(panel_of_normals_workflow): def test_purecn_step_part_get_output_files_coverage(panel_of_normals_workflow): """Tests PureCnStepPart._get_output_files_coverage()""" expected = { - "coverage": "work/{mapper}.purecn/out/{mapper}.{normal_library,.+-DNA[0-9]+-WES[0-9]+}_coverage_loess.txt.gz" + "coverage": "work/{mapper}.purecn/out/{mapper}.purecn.{library_name,.+-DNA[0-9]+-WES[0-9]+}_coverage_loess.txt.gz" } actual = panel_of_normals_workflow.get_output_files("purecn", "coverage") assert actual == expected @@ -556,7 +556,7 @@ def test_purecn_step_part_get_output_files_coverage(panel_of_normals_workflow): def test_purecn_step_part_get_log_file_coverage(panel_of_normals_workflow): """Tests PureCnStepPart._get_log_file_coverage()""" expected = get_expected_log_files_dict( - base_out="work/{mapper}.purecn/log/{mapper}.{normal_library,.+-DNA[0-9]+-WES[0-9]+}" + base_out="work/{mapper}.purecn/log/{mapper}.purecn.{library_name,.+-DNA[0-9]+-WES[0-9]+}" ) actual = panel_of_normals_workflow.get_log_file("purecn", "coverage") assert actual == expected @@ -567,8 +567,8 @@ def test_purecn_step_part_get_input_files_create_panel(panel_of_normals_workflow wildcards = Wildcards(fromdict={"mapper": "bwa"}) expected = { "normals": [ - "work/bwa.purecn/out/bwa.P001-N1-DNA1-WGS1_coverage_loess.txt.gz", - "work/bwa.purecn/out/bwa.P002-N1-DNA1-WGS1_coverage_loess.txt.gz", + "work/bwa.purecn/out/bwa.purecn.P001-N1-DNA1-WGS1_coverage_loess.txt.gz", + "work/bwa.purecn/out/bwa.purecn.P002-N1-DNA1-WGS1_coverage_loess.txt.gz", ], "container": "work/containers/out/purecn.simg", } diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_cnv_checking.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_cnv_checking.py index 2310f7676..92c42cabf 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_cnv_checking.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_cnv_checking.py @@ -167,8 +167,7 @@ def test_cnv_run_step_part_get_input_files(somatic_cnv_checking_workflow): fromdict={"mapper": "bwa", "caller": "cnvkit", "library_name": "P001-T1-DNA1-WGS1"} ) expected = { - "cnv": "CNV_CALLING/output/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.bed.gz", - "cnv_tbi": "CNV_CALLING/output/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1.bed.gz.tbi", + "cnv": "CNV_CALLING/output/bwa.cnvkit.P001-T1-DNA1-WGS1/out/bwa.cnvkit.P001-T1-DNA1-WGS1_dnacopy.seg", "normal": "work/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.normal.vcf.gz", "normal_tbi": "work/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.normal.vcf.gz.tbi", "tumor": "work/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.tumor.vcf.gz", diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_gene_fusion_calling_processed_fastq.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_gene_fusion_calling_processed_fastq.py index 9b1548360..798000023 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_gene_fusion_calling_processed_fastq.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_gene_fusion_calling_processed_fastq.py @@ -24,6 +24,8 @@ def minimal_config(): static_data_config: reference: path: /path/to/ref.fa + features: + path: /path/to/features.gtf step_config: ngs_mapping: @@ -49,7 +51,6 @@ def minimal_config(): path_dataset_directory: REQUIRED arriba: path_index: /path/to/star/index - features: /path/to/features.gtf data_sets: first_batch: diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py index 6704fbfcd..a05198407 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py @@ -482,12 +482,10 @@ def test_cnvkit_postprocess_step_part_get_input_files(somatic_targeted_seq_cnv_c def test_cnvkit_postprocess_step_part_get_output_files(somatic_targeted_seq_cnv_calling_workflow): - base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}.bed.gz" + base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}" expected = { - "final": base_name_out, - "final_tbi": base_name_out + ".tbi", - "final_md5": base_name_out + ".md5", - "final_tbi_md5": base_name_out + ".tbi.md5", + "final": base_name_out + "_dnacopy.seg", + "final_md5": base_name_out + "_dnacopy.seg.md5", } actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("cnvkit", "postprocess") assert actual == expected @@ -597,7 +595,13 @@ def test_cnvkit_export_step_part_get_output_files(somatic_targeted_seq_cnv_calli # Define expected expected = {} base_name_out = "work/{mapper}.cnvkit.{library_name}/out/{mapper}.cnvkit.{library_name}" - for key, ext in (("seg", "seg"), ("vcf", "vcf.gz"), ("tbi", "vcf.gz.tbi")): + for key, ext in ( + ("bed", "bed.gz"), + ("bed_tbi", "bed.gz.tbi"), + ("seg", "seg"), + ("vcf", "vcf.gz"), + ("vcf_tbi", "vcf.gz.tbi"), + ): expected[key] = base_name_out + "." + ext expected[key + "_md5"] = expected[key] + ".md5" # Get actual @@ -854,8 +858,8 @@ def test_sequenza_step_part_get_log_file_gcreference(somatic_targeted_seq_cnv_ca assert actual == expected -def test_sequenza_step_part_get_input_files_run(somatic_targeted_seq_cnv_calling_workflow): - """Tests SequenzaStepPart.get_input_files() - action 'run'""" +def test_sequenza_step_part_get_input_files_coverage(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_input_files() - action 'coverage'""" wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) expected = { "gc": "work/static_data/out/sequenza.50.wig.gz", @@ -864,58 +868,61 @@ def test_sequenza_step_part_get_input_files_run(somatic_targeted_seq_cnv_calling "tumor_bam": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam", "tumor_bai": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam.bai", } - actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("sequenza", "run")(wildcards) + actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("sequenza", "coverage")( + wildcards + ) assert actual == expected -def test_sequenza_step_part_get_output_files_run(somatic_targeted_seq_cnv_calling_workflow): - """Tests SequenzaStepPart.get_output_files() - action 'run'""" +def test_sequenza_step_part_get_output_files_coverage(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_output_files() - action 'coverage'""" + base_name = "{mapper}.sequenza.{library_name}" expected = { - "seqz": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz", - "seqz_md5": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz.md5", + "seqz": f"work/{base_name}/out/{base_name}.seqz.gz", + "seqz_md5": f"work/{base_name}/out/{base_name}.seqz.gz.md5", } - actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("sequenza", "run") + actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("sequenza", "coverage") assert actual == expected -def test_sequenza_step_part_get_log_file_run(somatic_targeted_seq_cnv_calling_workflow): - """Tests SequenzaStepPart.get_log_file() - action 'run'""" - base_name = "work/{mapper}.sequenza.{library_name}/log/{mapper}.sequenza.{library_name}.run" +def test_sequenza_step_part_get_log_file_coverage(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_log_file() - action 'coverage'""" + base_name = ( + "work/{mapper}.sequenza.{library_name}/log/{mapper}.sequenza.{library_name}.coverage" + ) expected = get_expected_log_files_dict(base_out=base_name) - actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("sequenza", "run") + actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("sequenza", "coverage") assert actual == expected -def test_sequenza_step_part_get_input_files_report(somatic_targeted_seq_cnv_calling_workflow): - """Tests SequenzaStepPart.get_input_files() - action 'report'""" +def test_sequenza_step_part_get_input_files_run(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_input_files() - action 'run'""" + wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) expected = { "packages": "work/R_packages/out/sequenza.done", "seqz": "work/{mapper}.sequenza.{library_name}/out/{mapper}.sequenza.{library_name}.seqz.gz", } - actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("sequenza", "report") - assert actual == expected - - -def test_sequenza_step_part_get_output_files_report(somatic_targeted_seq_cnv_calling_workflow): - """Tests SequenzaStepPart.get_output_files() - action 'report'""" - expected = {"done": "work/{mapper}.sequenza.{library_name}/report/.done"} - actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("sequenza", "report") + actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("sequenza", "run")(wildcards) assert actual == expected -def test_sequenza_step_part_get_params_report(somatic_targeted_seq_cnv_calling_workflow): - """Tests SequenzaStepPart.get_params() - action 'report'""" - wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) - expected = "P001-T1-DNA1-WGS1" - actual = somatic_targeted_seq_cnv_calling_workflow.get_params("sequenza", "report")(wildcards) +def test_sequenza_step_part_get_output_files_run(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_output_files() - action 'run'""" + base_name = "{mapper}.sequenza.{library_name}" + expected = { + "seg": f"work/{base_name}/out/{base_name}_dnacopy.seg", + "seg_md5": f"work/{base_name}/out/{base_name}_dnacopy.seg.md5", + "done": f"work/{base_name}/report/.done", + } + actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("sequenza", "run") assert actual == expected -def test_sequenza_step_part_get_log_file_report(somatic_targeted_seq_cnv_calling_workflow): - """Tests SequenzaStepPart.get_log_file() - action 'report'""" - base_name = "work/{mapper}.sequenza.{library_name}/log/{mapper}.sequenza.{library_name}.report" +def test_sequenza_step_part_get_log_file_run(somatic_targeted_seq_cnv_calling_workflow): + """Tests SequenzaStepPart.get_log_file() - action 'run'""" + base_name = "work/{mapper}.sequenza.{library_name}/log/{mapper}.sequenza.{library_name}.run" expected = get_expected_log_files_dict(base_out=base_name) - actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("sequenza", "report") + actual = somatic_targeted_seq_cnv_calling_workflow.get_log_file("sequenza", "run") assert actual == expected @@ -923,7 +930,8 @@ def test_sequenza_step_part_get_resource_usage_call(somatic_targeted_seq_cnv_cal """Tests SequenzaStepPart.get_resource_usage()""" # Define expected expected_dicts = { - "run": {"threads": 4, "time": "24:00:00", "memory": "16G", "partition": "medium"}, + "coverage": {"threads": 1, "time": "24:00:00", "memory": "24G", "partition": "medium"}, + "run": {"threads": 4, "time": "24:00:00", "memory": "64G", "partition": "medium"}, } # Evaluate for action, resources in expected_dicts.items(): @@ -953,9 +961,8 @@ def test_purecn_step_part_get_input_files_coverage(somatic_targeted_seq_cnv_call def test_purecn_step_part_get_output_files_coverage(somatic_targeted_seq_cnv_calling_workflow): """Tests PureCNStepPart.get_output_files() - action 'coverage'""" - expected = { - "coverage": "work/{mapper}.purecn.{library_name}/out/{mapper}.{library_name}_coverage_loess.txt.gz" - } + name_pattern = "{mapper}.purecn.{library_name}" + expected = {"coverage": f"work/{name_pattern}/out/{name_pattern}_coverage_loess.txt.gz"} actual = somatic_targeted_seq_cnv_calling_workflow.get_output_files("purecn", "coverage") assert actual == expected @@ -972,7 +979,7 @@ def test_purecn_step_part_get_input_files_run(somatic_targeted_seq_cnv_calling_w """Tests PureCNStepPart.get_input_files() - action 'run'""" wildcards = Wildcards(fromdict={"mapper": "bwa", "library_name": "P001-T1-DNA1-WGS1"}) expected = { - "tumor": "work/bwa.purecn.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1_coverage_loess.txt.gz", + "tumor": "work/bwa.purecn.P001-T1-DNA1-WGS1/out/bwa.purecn.P001-T1-DNA1-WGS1_coverage_loess.txt.gz", "vcf": "SOMATIC_VARIANT_CALLING/output/bwa.mutect2.P001-T1-DNA1-WGS1/out/bwa.mutect2.P001-T1-DNA1-WGS1.full.vcf.gz", } actual = somatic_targeted_seq_cnv_calling_workflow.get_input_files("purecn", "run")(wildcards) @@ -981,7 +988,7 @@ def test_purecn_step_part_get_input_files_run(somatic_targeted_seq_cnv_calling_w def test_purecn_step_part_get_output_files_run(somatic_targeted_seq_cnv_calling_workflow): """Tests PureCNStepPart.get_output_files() - action 'run'""" - base_name = "work/{mapper}.purecn.{library_name}/out/{library_name}" + base_name = "work/{mapper}.purecn.{library_name}/out/{mapper}.purecn.{library_name}" expected = { "segments": base_name + "_dnacopy.seg", "ploidy": base_name + ".csv", @@ -1039,10 +1046,12 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call assert actual == expected # Check result file construction + name_pattern = "bwa.{method}.P00{{i}}-T{{t}}-DNA1-WGS1" + # cnvetti tpl = ( - "output/bwa.cnvetti_on_target_coverage.P00{i}-T{t}-DNA1-WGS1/out/" - "bwa.cnvetti_on_target_coverage.P00{i}-T{t}-DNA1-WGS1.{ext}" + f"output/{name_pattern}/out/{name_pattern}".format(method="cnvetti_on_target_coverage") + + ".{ext}" ) expected = [ tpl.format(i=i, t=t, ext=ext) @@ -1050,8 +1059,8 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call for ext in ("bcf", "bcf.md5", "bcf.csi", "bcf.csi.md5") ] tpl = ( - "output/bwa.cnvetti_on_target_segment.P00{i}-T{t}-DNA1-WGS1/out/" - "bwa.cnvetti_on_target_segment.P00{i}-T{t}-DNA1-WGS1.{ext}" + f"output/{name_pattern}/out/{name_pattern}".format(method="cnvetti_on_target_segment") + + ".{ext}" ) expected += [ tpl.format(i=i, t=t, ext=ext) @@ -1068,8 +1077,8 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call ) ] tpl = ( - "output/bwa.cnvetti_on_target_postprocess.P00{i}-T{t}-DNA1-WGS1/out/" - "bwa.cnvetti_on_target_postprocess.P00{i}-T{t}-DNA1-WGS1_{ext}" + f"output/{name_pattern}/out/{name_pattern}".format(method="cnvetti_on_target_postprocess") + + "_{ext}" ) expected += [ tpl.format(i=i, t=t, ext=ext) @@ -1088,16 +1097,24 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call ) ] # cnvkit - tpl = "output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/out/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.{ext}{md5}" + tpl = f"output/{name_pattern}/out/{name_pattern}".format(method="cnvkit") + "{ext}{md5}" expected += [ tpl.format(i=i, t=t, ext=ext, md5=md5) for i, t in ((1, 1), (2, 1), (2, 2)) - for ext in ("cnr", "bed.gz", "bed.gz.tbi", "seg", "vcf.gz", "vcf.gz.tbi") + for ext in ( + ".cnr", + "_dnacopy.seg", + ".bed.gz", + ".bed.gz.tbi", + ".seg", + ".vcf.gz", + ".vcf.gz.tbi", + ) for md5 in ("", ".md5") ] tpl = ( - "output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/report/" - "bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.{plot}.{ext}{md5}" + f"output/{name_pattern}/report/{name_pattern}".format(method="cnvkit") + + ".{plot}.{ext}{md5}" ) expected += [ tpl.format(i=i, t=t, plot=plot, ext=ext, md5=md5) @@ -1106,8 +1123,8 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call for md5 in ("", ".md5") ] tpl = ( - "output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/report/" - "bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.{plot}.chr{chrom}.{ext}{md5}" + f"output/{name_pattern}/report/{name_pattern}".format(method="cnvkit") + + ".{plot}.chr{chrom}.{ext}{md5}" ) expected += [ tpl.format(i=i, t=t, plot=plot, ext=ext, chrom=str(chrom), md5=md5) @@ -1117,8 +1134,8 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call for md5 in ("", ".md5") ] tpl = ( - "output/bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1/report/" - "bwa.cnvkit.P00{i}-T{t}-DNA1-WGS1.{report}.txt{md5}" + f"output/{name_pattern}/report/{name_pattern}".format(method="cnvkit") + + ".{report}.txt{md5}" ) expected += [ tpl.format(i=i, t=t, report=report, md5=md5) @@ -1127,28 +1144,22 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call for md5 in ("", ".md5") ] # copywriter - tpl = ( - "output/bwa.copywriter.P00{i}-T{t}-DNA1-WGS1/out/" - "bwa.copywriter.P00{i}-T{t}-DNA1-WGS1_{ext}" - ) + tpl = f"output/{name_pattern}/out/{name_pattern}".format(method="copywriter") + "_{ext}{md5}" expected += [ - tpl.format(i=i, t=t, ext=ext) + tpl.format(i=i, t=t, ext=ext, md5=md5) for i, t in ((1, 1), (2, 1), (2, 2)) for ext in ( "bins.txt", "gene_call.txt", "gene_log2.txt", "segments.txt", - "bins.txt.md5", - "gene_call.txt.md5", - "gene_log2.txt.md5", - "segments.txt.md5", ) + for md5 in ("", ".md5") ] # purecn - tpl = "output/bwa.purecn.P00{i}-T{t}-DNA1-WGS1/out/P00{i}-T{t}-DNA1-WGS1{ext}{checksum}" + tpl = f"output/{name_pattern}/out/{name_pattern}".format(method="purecn") + "{ext}{md5}" expected += [ - tpl.format(i=i, t=t, ext=ext, checksum=checksum) + tpl.format(i=i, t=t, ext=ext, md5=md5) for i, t in ((1, 1), (2, 1), (2, 2)) for ext in ( ".csv", @@ -1158,18 +1169,18 @@ def test_somatic_targeted_seq_cnv_calling_workflow(somatic_targeted_seq_cnv_call "_amplification_pvalues.csv", "_loh.csv", ) - for checksum in ("", ".md5") + for md5 in ("", ".md5") ] # sequenza - tpl = ( - "output/bwa.sequenza.P00{i}-T{t}-DNA1-WGS1/out/" - "bwa.sequenza.P00{i}-T{t}-DNA1-WGS1.seqz.gz{checksum}" - ) + tpl = f"output/{name_pattern}/out/{name_pattern}".format(method="sequenza") + "{ext}{md5}" expected += [ - tpl.format(i=i, t=t, checksum=checksum) + tpl.format(i=i, t=t, ext=ext, md5=md5) for i, t in ((1, 1), (2, 1), (2, 2)) - for checksum in ("", ".md5") + for ext in ("_dnacopy.seg", ".seqz.gz") + for md5 in ("", ".md5") ] + tpl = f"output/{name_pattern}/report/.done".format(method="sequenza") + expected += [tpl.format(i=i, t=t) for i, t in ((1, 1), (2, 1), (2, 2))] expected = list(sorted(expected)) actual = list(sorted(somatic_targeted_seq_cnv_calling_workflow.get_result_files())) # HACK TODO diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_annotation.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_annotation.py index d6f0731d8..78eba204d 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_annotation.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_annotation.py @@ -113,8 +113,8 @@ def test_jannovar_step_part_get_input_files(somatic_variant_annotation_workflow) def test_jannovar_step_part_get_output_files(somatic_variant_annotation_workflow): """Tests JannovarAnnotateSomaticVcfStepPart.get_output_files()""" base_out = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.{tumor_library}/out/" - "{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.{tumor_library}" + "work/{mapper}.{var_caller}.jannovar.{tumor_library}/out/" + "{mapper}.{var_caller}.jannovar.{tumor_library}" ) expected = get_expected_output_vcf_files_dict(base_out=base_out) actual = somatic_variant_annotation_workflow.get_output_files( @@ -126,8 +126,8 @@ def test_jannovar_step_part_get_output_files(somatic_variant_annotation_workflow def test_jannovar_step_part_get_log_file(somatic_variant_annotation_workflow): """Tests JannovarAnnotateSomaticVcfStepPart.get_output_files()""" base_out = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.{tumor_library}/log/" - "{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.{tumor_library}" + "work/{mapper}.{var_caller}.jannovar.{tumor_library}/log/" + "{mapper}.{var_caller}.jannovar.{tumor_library}" ) expected = get_expected_log_files_dict(base_out=base_out) actual = somatic_variant_annotation_workflow.get_log_file("jannovar", "annotate_somatic_vcf") @@ -240,7 +240,7 @@ def test_somatic_variant_annotation_workflow(somatic_variant_annotation_workflow for ext in ("vcf.gz", "vcf.gz.md5", "vcf.gz.tbi", "vcf.gz.tbi.md5") for mapper in ("bwa",) for var_caller in ("mutect", "scalpel") - for annotator in ("jannovar_annotate_somatic_vcf", "vep") + for annotator in ("jannovar", "vep") ] expected += [ tpl.format( @@ -267,7 +267,7 @@ def test_somatic_variant_annotation_workflow(somatic_variant_annotation_workflow ) for mapper in ("bwa",) for var_caller in ("mutect", "scalpel") - for annotator in ("jannovar_annotate_somatic_vcf", "vep") + for annotator in ("jannovar", "vep") ] expected = list(sorted(expected)) actual = list(sorted(somatic_variant_annotation_workflow.get_result_files())) diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py index d8dfabe72..200f25651 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py @@ -34,6 +34,7 @@ def minimal_config(): somatic_variant_filtration: tools_ngs_mapping: ['bwa'] tools_somatic_variant_calling: ['mutect2'] + tools_somatic_variant_annotation: ['jannovar'] data_sets: first_batch: @@ -82,8 +83,8 @@ def test_dkfz_bias_filter_step_part_get_input_files(somatic_variant_filtration_w """Tests DkfzBiasFilterStepPart.get_input_files()""" somatic_base_out = ( "SOMATIC_VARIANT_ANNOTATION/output/" - "{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.{tumor_library}/out/" - "{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.{tumor_library}" + "{mapper}.{var_caller}.{annotator}.{tumor_library}/out/" + "{mapper}.{var_caller}.{annotator}.{tumor_library}" ) expected = { "vcf": somatic_base_out + ".vcf.gz", @@ -98,8 +99,8 @@ def test_dkfz_bias_filter_step_part_get_input_files(somatic_variant_filtration_w def test_dkfz_bias_filter_step_part_get_output_files(somatic_variant_filtration_workflow): """Tests DkfzBiasFilterStepPart.get_output_files()""" base_out = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter." - "{tumor_library,[^\\.]+}/out/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter." + "{tumor_library,[^\\.]+}/out/{mapper}.{var_caller}.{annotator}." "dkfz_bias_filter.{tumor_library}" ) expected = get_expected_output_vcf_files_dict(base_out=base_out) @@ -110,8 +111,8 @@ def test_dkfz_bias_filter_step_part_get_output_files(somatic_variant_filtration_ def test_dkfz_bias_filter_step_part_get_log_file(somatic_variant_filtration_workflow): """Tests DkfzBiasFilterStepPart.get_log_file()""" base_out = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.{tumor_library}/" - "log/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.{tumor_library}" + "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.{tumor_library}/" + "log/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.{tumor_library}" ) expected = get_expected_log_files_dict(base_out=base_out) actual = somatic_variant_filtration_workflow.get_log_file("dkfz_bias_filter", "run") @@ -137,11 +138,16 @@ def test_dkfz_bias_filter_step_part_get_resource_usage(somatic_variant_filtratio def test_eb_filter_step_part_get_input_files_run(somatic_variant_filtration_workflow): """Tests EbFilterStepPart._get_input_files_run()""" wildcards = Wildcards( - fromdict={"mapper": "bwa", "var_caller": "mutect2", "tumor_library": "P001-T1-DNA1-WGS1"} + fromdict={ + "mapper": "bwa", + "var_caller": "mutect2", + "annotator": "jannovar", + "tumor_library": "P001-T1-DNA1-WGS1", + } ) base_out = ( - "work/bwa.mutect2.jannovar_annotate_somatic_vcf.dkfz_bias_filter.P001-T1-DNA1-WGS1/out/" - "bwa.mutect2.jannovar_annotate_somatic_vcf.dkfz_bias_filter.P001-T1-DNA1-WGS1" + "work/bwa.mutect2.jannovar.dkfz_bias_filter.P001-T1-DNA1-WGS1/out/" + "bwa.mutect2.jannovar.dkfz_bias_filter.P001-T1-DNA1-WGS1" ) expected = { "vcf": base_out + ".vcf.gz", @@ -177,8 +183,8 @@ def test_eb_filter_step_part_get_input_files_write_panel(somatic_variant_filtrat def test_eb_filter_step_part_get_output_files_run(somatic_variant_filtration_workflow): """Tests EbFilterStepPart._get_output_files_run()""" base_out = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter." - "eb_filter.{tumor_library,[^\\.]+}/out/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter." + "eb_filter.{tumor_library,[^\\.]+}/out/{mapper}.{var_caller}.{annotator}." "dkfz_bias_filter.eb_filter.{tumor_library}" ) expected = get_expected_output_vcf_files_dict(base_out=base_out) @@ -200,8 +206,8 @@ def test_eb_filter_step_part_get_output_files_write_panel(somatic_variant_filtra def test_eb_eb_filter_step_part_get_log_file_run(somatic_variant_filtration_workflow): """Tests EbFilterStepPart._get_log_file_run()""" base_out = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." - "{tumor_library}/log/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter." + "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.eb_filter." + "{tumor_library}/log/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter." "eb_filter.{tumor_library}" ) expected = get_expected_log_files_dict(base_out=base_out) @@ -236,8 +242,8 @@ def test_eb_filter_step_part_get_resource_usage(somatic_variant_filtration_workf def test_apply_filters_step_part_get_input_files(somatic_variant_filtration_workflow): """Tests ApplyFiltersStepPart.get_input_files()""" base_out = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." - "{tumor_library}/out/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." + "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.eb_filter." + "{tumor_library}/out/{mapper}.{var_caller}.{annotator}." "dkfz_bias_filter.eb_filter.{tumor_library}" ) expected = { @@ -251,9 +257,9 @@ def test_apply_filters_step_part_get_input_files(somatic_variant_filtration_work def test_apply_filters_step_part_get_output_files(somatic_variant_filtration_workflow): """Tests ApplyFiltersStepPart.get_output_files()""" base_out = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." + "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.eb_filter." "{tumor_library}.{filter_set}.genome_wide/out/{mapper}.{var_caller}." - "jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." + "{annotator}.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." "genome_wide" ) expected = get_expected_output_vcf_files_dict(base_out=base_out) @@ -264,9 +270,9 @@ def test_apply_filters_step_part_get_output_files(somatic_variant_filtration_wor def test_apply_filters_step_part_get_log_file(somatic_variant_filtration_workflow): """Tests ApplyFiltersStepPart.get_log_file()""" expected = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." + "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.eb_filter." "{tumor_library}.{filter_set}.genome_wide/log/{mapper}.{var_caller}." - "jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." + "{annotator}.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." "genome_wide.log" ) actual = somatic_variant_filtration_workflow.get_log_file("apply_filters", "run") @@ -299,8 +305,8 @@ def test_apply_filters_step_part_get_resource_usage(somatic_variant_filtration_w # } # ) # base_out = ( -# "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." -# "{tumor_library}/out/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf." +# "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.eb_filter." +# "{tumor_library}/out/{mapper}.{var_caller}.{annotator}." # "dkfz_bias_filter.eb_filter.{tumor_library}" # ) # expected = { @@ -315,9 +321,9 @@ def test_apply_filters_step_part_get_resource_usage(somatic_variant_filtration_w def test_filter_to_exons_step_part_get_output_files(somatic_variant_filtration_workflow): """Tests FilterToExonsStepPart.get_output_files()""" base_out = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." + "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter.eb_filter." "{tumor_library}.{filter_set}.{exon_list}/out/{mapper}.{var_caller}." - "jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." + "{annotator}.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." "{exon_list}" ) expected = get_expected_output_vcf_files_dict(base_out=base_out) @@ -328,9 +334,9 @@ def test_filter_to_exons_step_part_get_output_files(somatic_variant_filtration_w def test_filter_to_exons_step_part_get_log_file(somatic_variant_filtration_workflow): """Tests FilterToExonsStepPart.get_log_file()""" expected = ( - "work/{mapper}.{var_caller}.jannovar_annotate_somatic_vcf.dkfz_bias_filter." + "work/{mapper}.{var_caller}.{annotator}.dkfz_bias_filter." "eb_filter.{tumor_library}.{filter_set}.{exon_list}/log/{mapper}.{var_caller}." - "jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." + "{annotator}.dkfz_bias_filter.eb_filter.{tumor_library}.{filter_set}." "{exon_list}.log" ) actual = somatic_variant_filtration_workflow.get_log_file("filter_to_exons", "run") @@ -362,9 +368,9 @@ def test_somatic_variant_filtration_workflow(somatic_variant_filtration_workflow # Check result file construction tpl = ( - "output/bwa.mutect2.jannovar_annotate_somatic_vcf.dkfz_bias_filter." + "output/bwa.mutect2.jannovar.dkfz_bias_filter." "eb_filter.P00{i}-T{t}-DNA1-WGS1.{filter}/out/" - "bwa.mutect2.jannovar_annotate_somatic_vcf.dkfz_bias_filter.eb_filter." + "bwa.mutect2.jannovar.dkfz_bias_filter.eb_filter." "P00{i}-T{t}-DNA1-WGS1.{filter}.{ext}" ) expected = [ diff --git a/tests/snappy_wrappers/wrappers/data/mutect2_par_run.snakemake b/tests/snappy_wrappers/wrappers/data/mutect2_par_run.snakemake index 558131679..795c0b5c0 100644 --- a/tests/snappy_wrappers/wrappers/data/mutect2_par_run.snakemake +++ b/tests/snappy_wrappers/wrappers/data/mutect2_par_run.snakemake @@ -97,7 +97,7 @@ def resource_chunk_memory(wildcards, attempt): def resource_chunk_time(wildcards, attempt): '''Return the time to use for running one chunk.''' - return multiply_time('3:00:00', attempt) + return multiply_time('12:00:00', attempt) rule all: diff --git a/tests/snappy_wrappers/wrappers/test_install_R_package.py b/tests/snappy_wrappers/wrappers/test_install_R_package.py new file mode 100644 index 000000000..8b6155f5b --- /dev/null +++ b/tests/snappy_wrappers/wrappers/test_install_R_package.py @@ -0,0 +1,52 @@ +# -*- coding: utf-8 -*- +"""Code for testing the R package installation helper function""" + +from snappy_wrappers.utils import install_R_package + + +def test_install_R_package(mocker, fp): + """Tests install_R_package""" + mocker.patch("snappy_wrappers.utils.os.makedirs", return_value=True) + packages = [ + { + "name": "cran", + "repo": "cran", + "install": "install.packages('{}', lib='/path/to/lib', update=FALSE, ask=FALSE)", + "check": "find.package('cran', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)", + }, + { + "name": "bioc", + "repo": "bioconductor", + "install": "BiocManager::install('{}', lib='/path/to/lib', update=FALSE, ask=FALSE)", + "check": "find.package('bioc', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)", + }, + { + "name": "username/package/subdir@*rel.ea.se", + "repo": "github", + "install": "remotes::install_github('{}', lib='/path/to/lib', upgrade='never')", + "check": "find.package('package', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)", + }, + { + "name": "username/package/subdir@ref", + "repo": "bitbucket", + "install": "remotes::install_bitbucket('{}', lib='/path/to/lib', upgrade='never')", + "check": "find.package('package', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)", + }, + { + "name": "/path/to/package.tar.gz", + "repo": "local", + "install": "remotes::install_local('{}', lib='/path/to/lib', upgrade='never')", + "check": "find.package('package', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)", + }, + ] + for package in packages: + script = "; ".join( + [ + package["install"].format(package["name"]), + "status <- try({})".format(package["check"]), + "status <- ifelse(is(status, 'try-error'), 1, 0)", + "quit(save='no', status=status, runLast=FALSE)", + ] + ) + fp.register_subprocess(["R", "--vanilla", "-e", script], stdout="") + install_R_package(dest="/path/to/lib", name=package["name"], repo=package["repo"]) diff --git a/tests/snappy_wrappers/wrappers/test_mutect2_par_run.py b/tests/snappy_wrappers/wrappers/test_mutect2_par_run.py index 023e51bcd..8c4eec0c3 100644 --- a/tests/snappy_wrappers/wrappers/test_mutect2_par_run.py +++ b/tests/snappy_wrappers/wrappers/test_mutect2_par_run.py @@ -283,11 +283,11 @@ def test_mutect2_wrapper_run_preamble_resource_chunk_time(construct_preamble_mod """ # Define (input, expected) pair input_expected_pairs = ( - (1, "0-03:00:00"), - (2, "0-06:00:00"), - (3, "0-09:00:00"), - (4, "0-12:00:00"), - (5, "0-15:00:00"), + (1, "0-12:00:00"), + (2, "1-00:00:00"), + (3, "1-12:00:00"), + (4, "2-00:00:00"), + (5, "2-12:00:00"), ) # Test all pairs for pair in input_expected_pairs: