3 commits

Author	SHA1	Message	Date
Rike	6a4732ef3b	similar issues arise with bqsrspark, also use broadinstitute container	2022-06-09 15:29:00 +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