feat: make germline variants pon optional for mutect2 #375
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…mon variants
the workflow is dependent on the presence of a path to the common variants vcf
minor bug fixes have also been made to the list output files for mutect & scalpel
tests have been adapted to reflect the bug fixes
fix: log and checksums properly handled
Implementation: generic parallel wrapper, which copies all output & log files as requested by the snakemake output
The generic wrapper also creates a tar file with all chunks logs (not linked to output yet)
Tests have been amended to exercise the complete creation of the parallel snakemake file
ericblanc20
changed the title
mbenary
approved these changes
Feb 20, 2023
ericblanc20
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369-make-germline-variants-pon-optional-for-mutect2
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This was referenced Dec 9, 2024
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The pull request is more ambitious than expected.
The reason is the need for keeping chunk logs, which are missing for multiple parallelised steps (such as the somatic variant annotations & filtering).
To solve this problem in a generic way, a new abstract class (currently called
ParallelMutect2BaseWrapper) has been created for parallelisation.It is organised in the following way: the class collects the file names of all outputs & all log files that are stored in the snakemake object. The class then writes a Snakefile, such that each chunk should create all the requested output & log files. The class then merges the log files, and delegates the merging of output files to any derived class.
In this way, the class which parallelise
Mutect2output just needs to define how to merge the different types of files produced byMutect2(the vcf, of course, but also files necessary for filtering results (orientation stats, ...)).All other opreations (intervals splitting, Snakefile creation, dynamic resource increase, ...) are taken care of by the
ParallelMutect2BaseWrapperparent class.The tests have also been extensively re-worked to improve coverage (hopefully).
The changes required to remove the requirements on the existence of a panel of normal, a germline resource and a list of common variants are a bit drowned in the other changes.
They are limited to
Snakefile&__init__.pyin thesomatic_variant_callingworkflow directory, and to thefilterwrapper in themutect2list of wrappers.