Documentation #3
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* add ref data for pcgr 2.2.1 * add vep path pcgr * edit refdata path for vep pcgr * update pcgr report name name * change path VEP ref data * update container version * remove VEP version * change bolt version to test
* add process and config for vcf2maf * fix path vep data * remove duplicate * fix and linting * remove params from VCF2MAF process * fix and simplify process * add meta.key to channel * add genome build as input * add dockerfile * Make sigrap (HRDetect, MutationalPatterns) individual process (#16) * remove trace of genome build and hardcode in VCF2MAF * use biocontainers container for vcf2maf * remove string interpolation * change to stub no version template * revert deleted line
* change sigrap container * change cancer report container * latest bolt version * update meta id sigrap * bump sigrap * remove print * restaure metadata sigrap * change multiqc container * add param for pcgr chunck size * add mutpat predefined dbs argument * update container * add back formating comment
* fix channel prepare reference * refactor tarball extraction to use proper channel patterns. Follow oncoanalyser pattern for tarball extraction with .collect() and .map() * adapte extraction tarball to match pcgr expected vep structure * fix dir name extract tarball for VEP * change to adapt strip compoment for pcgr data
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