Maxime Borry b399f22af2 Add new module: cmseq/polymut (#918) ... * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * first cmseq commit * compressing and removing not reproducible md5sums * save intermediate work * follow symlinks while decompressing * add cmseq/polymut * add polymut * add extra test with optional input file * remove metabat2 * Update modules/cmseq/polymut/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix file extension * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add test without bam index * split tests in workflows * answer PR review * report version from variable Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-11-09 16:12:51 +01:00
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polymut	Add new module: cmseq/polymut (#918)	2021-11-09 16:12:51 +01:00