feat: Added support for scarHRD (#429)

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,

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")