7 commits

Author	SHA1	Message	Date
nickhsmith	edfe28a5e0	Variant recalibration (#1885) ... * update tests * update * update * make the manta inputs consistant for germline/somatic/tumoronly * match chromosomes to cram file (chr21) * undo genotypegvfs * undo genotypegvfs * update VariantRecalibrator * lint * add '--resource:' tag Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-07-15 09:21:34 +02:00
Rike	169b2b96c1	update gatk version	2022-05-12 15:45:21 +02:00
Maxime U. Garcia	409af2f27c	Improve syntax/logic coherence in all gatk4 plugins (#1459) ... * feat: code polishing * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * code polishing * more code polishing * code polishing * tests for applybqsrspark * fix typo * no need to check md5sum for versions.yml * fix: use correct syntax * code polishing again * add tests for markduplicatesspark * simplify mergevcfs tests * add tests for baserecalibratorspark * fix: path to entry * code polishing * fix linting * simplify module * update meta.yml * fix pair mode * fix: MITO mode * more tests * fix command * bad copy paste * fix typos * fix tests * fix test * update meta.yml * correct versions.yml in all test.yml * code polishing * code polishing * more code polishing * fix args * add tmpdir for all Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-04-12 17:15:39 +02:00
FriederikeHanssen	967fb22ded	Update versions (#1292) ... * Update versions * update checksums + remove variables as input for applyvqsr * sneak in removal of values and provide them via modules.config * update another checksum * more checksums * move vairable to config * remove controlfreec, wrong branch * add line break	2022-02-15 11:29:36 +01:00
Mahesh Binzer-Panchal	e20e57f90b	Add when: block (#1261)	2022-02-04 09:53:32 +01:00
FriederikeHanssen	598d7abdb2	Log4j again (#1202) ... * Log4j again * Update checksums	2022-01-12 13:55:54 +01:00
GCJMackenzie	54e0ac4ed9	add module: Variantrecalibrator (#1088) ... * committing to pull updated nf-core files * saving changes to checout other branch * committing progress so far, difficulty with test data * uploading to be used as draft PR * fix linting error in meta.yml * attempt to group reference inputs together * updated input format for resources * meta.yml updated with new resource names * added output channel for recal index * module only takes single vcf file input now * committing to checkout * update to new syntax, remove indel test for now * updated to use memory options and new test data * Update modules/gatk4/variantrecalibrator/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update main.nf * Update modules/gatk4/variantrecalibrator/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * remove duplicate test keys from test_data.config Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2021-12-16 10:54:49 +00:00