FriederikeHanssen 19035c99d1 Add thread option to samtools modules (#1069) ... * add thread option to samtools modules * fix tests * fix tests * fix tests * Fix naming to fix tests * cpus-1 to account for mainthread * remove thread in ampliconclip, docu doesn't report this param * add -1 to all other applicable samtools modules * Update samtools version * Update checksums * retrigger GHA after update * Update modules/samtools/fastq/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/flagstat/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/index/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/merge/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/stats/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/view/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Fix md5sum fixmate * Fix md5sums * sth funny with the fixmate checksums * more md5sums updates Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>		2021-11-18 22:24:47 +01:00
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ampliconclip	Add thread option to samtools modules (#1069)	2021-11-18 22:24:47 +01:00
bam2fq	Bam2fq (#958)	2021-10-29 10:46:34 +02:00
depth	add new module samtools/depth (#950)	2021-10-28 12:53:21 +02:00
faidx	Fix version commands (#749)	2021-09-27 22:10:37 +01:00
fastq	nf-core modules bump-versions for all modules (#630)	2021-07-28 09:10:44 +01:00
fixmate	Add thread option to samtools modules (#1069)	2021-11-18 22:24:47 +01:00
flagstat	nf-core modules bump-versions for all modules (#630)	2021-07-28 09:10:44 +01:00
idxstats	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
index	Add thread option to samtools modules (#1069)	2021-11-18 22:24:47 +01:00
merge	Add thread option to samtools modules (#1069)	2021-11-18 22:24:47 +01:00
mpileup	nf-core modules bump-versions for all modules (#630)	2021-07-28 09:10:44 +01:00
sort	Add thread option to samtools modules (#1069)	2021-11-18 22:24:47 +01:00
stats	Add thread option to samtools modules (#1069)	2021-11-18 22:24:47 +01:00
view	Update to allow cram + update needed to use the gatk4 modules in sarek (#976)	2021-10-29 13:01:05 +02:00