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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -5,6 +5,11 @@ | |
| whole genomes, exomes or large panels). MANTIS starts from the aligned reads | ||
| (thus off ``ngs_mapping``) and generates a result file per tumor/normal pair. | ||
| As MANTIS is not maintained anymore, the pipeline now supports only | ||
| `MANTIS2 <https://github.com/nh13/MANTIS2>`_. | ||
| The new version appears to be very silimar to the old one, both in terms of input & output files, | ||
| and in terms of requirements. | ||
| ========== | ||
| Step Input | ||
| ========== | ||
|
|
@@ -19,13 +24,13 @@ | |
| .. note:: Tool-Specific Output | ||
| As the only integrated tool is MANTIS at the moment, the output is very tailored to the result | ||
| As the only integrated tool is MANTIS2 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. | ||
| - ``mantis.{mapper}.{lib_name}-{lib_pk}/out/`` | ||
| - ``mantis.{mapper}.{lib_name}-{lib_pk}.results.txt`` | ||
| - ``mantis.{mapper}.{lib_name}-{lib_pk}.results.txt.status`` | ||
| - ``{mapper}.mantis_msi2.{lib_name}-{lib_pk}/out/`` | ||
| - ``{mapper}.mantis_msi2.{lib_name}-{lib_pk}.results.txt`` | ||
| - ``{mapper}.mantis_msi2.{lib_name}-{lib_pk}.results.txt.status`` | ||
| ===================== | ||
| Default Configuration | ||
|
|
@@ -39,14 +44,15 @@ | |
| Available Somatic Targeted CNV Caller | ||
| ===================================== | ||
| - ``mantis`` | ||
| - ``mantis_msi2`` | ||
| """ | ||
|
|
||
| from collections import OrderedDict | ||
| import os | ||
| 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 | ||
|
|
@@ -60,30 +66,50 @@ | |
|
|
||
| __author__ = "Clemens Messerschmidt <[email protected]>" | ||
|
|
||
| #: Extensions of files to create as main payload | ||
| EXT_VALUES = (".results.txt", ".results.txt.status", ".results.txt.md5", ".results.txt.status.md5") | ||
|
|
||
| #: Names of the files to create for the extension | ||
| EXT_NAMES = ("result", "status", "result_md5", "status_md5") | ||
|
|
||
| EXT_MATCHED = { | ||
| "mantis_msi2": { | ||
| "result": ".results.txt", | ||
| "status": ".results.txt.status", | ||
| "result_md5": ".results.txt.md5", | ||
| "status_md5": ".results.txt.status.md5", | ||
| }, | ||
| } | ||
|
|
||
| #: Available somatic variant callers assuming matched samples. | ||
| MSI_CALLERS_MATCHED = ("mantis_msi2",) | ||
|
|
||
|
|
||
| #: Default configuration for the somatic_msi_calling step | ||
| DEFAULT_CONFIG = r""" | ||
| # Default configuration somatic_msi_calling | ||
| step_config: | ||
| somatic_msi_calling: | ||
| tools: ['mantis'] # REQUIRED - available: 'mantis' | ||
| tools: ['mantis_msi2'] # REQUIRED - available: 'mantis_msi2' | ||
| path_ngs_mapping: ../ngs_mapping # REQUIRED | ||
| loci_bed: /fast/groups/cubi/projects/biotools/Mantis/appData/hg19/loci.bed # REQUIRED | ||
| loci_bed: "" # REQUIRED | ||
| # hg19: /fast/work/groups/cubi/projects/biotools/Mantis/appData/hg19/loci.bed | ||
| # hg38: /fast/work/groups/cubi/projects/biotools/Mantis/appData/hg38/GRCh38.d1.vd1.all_loci.bed | ||
| """ | ||
|
|
||
|
|
||
| class MantisStepPart(BaseStepPart): | ||
| """Perform somatic microsatellite instability with MANTIS""" | ||
| class Mantis2StepPart(BaseStepPart): | ||
| """Perform somatic microsatellite instability with MANTIS_msi2""" | ||
|
|
||
| #: Step name | ||
| name = "mantis" | ||
| name = "mantis_msi2" | ||
|
|
||
| #: Class available actions | ||
| actions = ("run",) | ||
|
|
||
| def __init__(self, parent): | ||
| super().__init__(parent) | ||
| self.base_path_out = ( | ||
| "work/mantis.{{mapper}}.{{library_name}}/out/" "mantis.{{mapper}}.{{library_name}}{ext}" | ||
| "work/{{mapper}}.{msi_caller}.{{tumor_library}}/out/" | ||
| "{{mapper}}.{msi_caller}.{{tumor_library}}{ext}" | ||
| ) | ||
| # Build shortcut from cancer bio sample name to matched cancer sample | ||
| self.tumor_ngs_library_to_sample_pair = OrderedDict() | ||
|
|
@@ -92,12 +118,10 @@ def __init__(self, parent): | |
| 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): | ||
| # Validate action | ||
| self._validate_action(action) | ||
|
|
||
| def input_function(wildcards): | ||
| """Helper wrapper function""" | ||
| # Get shorcut to Snakemake sub workflow | ||
|
|
@@ -110,7 +134,7 @@ def input_function(wildcards): | |
| ) | ||
| ) | ||
| tumor_base_path = ( | ||
| "output/{mapper}.{library_name}/out/" "{mapper}.{library_name}" | ||
| "output/{mapper}.{tumor_library}/out/" "{mapper}.{tumor_library}" | ||
| ).format(**wildcards) | ||
| return { | ||
| "normal_bam": ngs_mapping(normal_base_path + ".bam"), | ||
|
|
@@ -119,24 +143,38 @@ def input_function(wildcards): | |
| "tumor_bai": ngs_mapping(tumor_base_path + ".bam.bai"), | ||
| } | ||
|
|
||
| assert action == "run", "Unsupported actions" | ||
| return input_function | ||
|
|
||
| @dictify | ||
| 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_output_files(self, action): | ||
| assert action == "run", "Unsupported actions" | ||
| exts = {"result": "results.txt", "status": "results.txt.status"} | ||
| for key, ext in exts.items(): | ||
| yield key, ( | ||
| "work/mantis.{{mapper}}.{{library_name}}/out/" | ||
| "mantis.{{mapper}}.{{library_name}}_{sfx}" | ||
| ).format(sfx=ext) | ||
|
|
||
| @staticmethod | ||
| def get_log_file(action): | ||
| """Return path to log file for the given action""" | ||
| _ = action | ||
| return "work/mantis.{mapper}.{library_name}/log/snakemake.mantis_run.log" | ||
| # Validate action | ||
| self._validate_action(action) | ||
| return dict( | ||
| zip(EXT_NAMES, expand(self.base_path_out, msi_caller=[self.name], ext=EXT_VALUES)) | ||
| ) | ||
|
|
||
| @dictify | ||
| def _get_log_file(self, action): | ||
| """Return dict of log files.""" | ||
| # Validate action | ||
| self._validate_action(action) | ||
|
|
||
| prefix = ( | ||
| "work/{{mapper}}.{msi_caller}.{{tumor_library}}/log/" | ||
| "{{mapper}}.{msi_caller}.{{tumor_library}}" | ||
| ).format(msi_caller=self.__class__.name) | ||
| 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 | ||
|
|
@@ -150,7 +188,7 @@ def get_resource_usage(self, action): | |
| self._validate_action(action) | ||
| return ResourceUsage( | ||
| threads=3, | ||
| time="08:00:00", # 2 hours | ||
| time="08:00:00", # 8 hours | ||
| memory=f"{30 * 1024 * 3}M", | ||
| ) | ||
|
|
||
|
|
@@ -164,9 +202,13 @@ class SomaticMsiCallingWorkflow(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""" | ||
| """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): | ||
|
|
@@ -179,14 +221,41 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir) | |
| (NgsMappingWorkflow,), | ||
| ) | ||
| # Register sub step classes so the sub steps are available | ||
| self.register_sub_step_classes((MantisStepPart, LinkOutStepPart)) | ||
| self.register_sub_step_classes((Mantis2StepPart, 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 = {"mantis": ("run",)} | ||
| """Return list of result files for the MSI calling workflow""" | ||
| name_pattern = "{mapper}.{msi_caller}.{tumor_library.name}" | ||
| for msi_caller in set(self.config["tools"]) & set(MSI_CALLERS_MATCHED): | ||
| yield from self._yield_result_files_matched( | ||
| os.path.join("output", name_pattern, "out", name_pattern + "{ext}"), | ||
| mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"], | ||
| msi_caller=msi_caller, | ||
| ext=EXT_MATCHED[msi_caller].values() if msi_caller in EXT_MATCHED else 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"]["ngs_mapping"]["tools"]["dna"], | ||
| msi_caller=msi_caller, | ||
| 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. | ||
| This function returns the results from the matched msi callers such as | ||
| mantis. | ||
| """ | ||
| for sheet in filter(is_not_background, self.shortcut_sheets): | ||
| for sample_pair in sheet.all_sample_pairs: | ||
| if ( | ||
|
|
@@ -199,21 +268,9 @@ def get_result_files(self): | |
| ) | ||
| 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/") | ||
| yield from expand( | ||
| tpl, tumor_library=[sample_pair.tumor_sample.dna_ngs_library], **kwargs | ||
| ) | ||
|
|
||
| def check_config(self): | ||
| """Check that the necessary globalc onfiguration is present""" | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,5 +2,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - numpy ==1.6.2 | ||
| - pysam ==0.8.3 | ||
| - mantis-msi2 | ||
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