3 commits

Author	SHA1	Message	Date
Matthias De Smet	36049bf544	Fgbio/fastqtobam (#1980) ... * fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-09-05 11:57:55 +02:00
Matthias Hörtenhuber	e745e167c1	Fix formatting in yaml files, add yamllint config (#1279) ... * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-02-15 11:15:27 +00:00
Francesco L	a0bc08732c	Rewritten module fgbio/fastqtobam (#916) ... * added template for fastqtobam * porting old code into new template * update with missing getprocessname function * test completed - updating all * fixed linting issues * improved reading Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2021-10-27 19:06:06 +02:00