2 commits

Author	SHA1	Message	Date
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
Johnathan D	2e619add87	Add samtools ampliconclip (#590) ... * created template for `samtools/ampliconclip` (#584) * All tests passing (#584) * Linting fixed (#584) * Final linting fixed (#584) * Optional output flags moved to `input` (#584) * typo fix (#584) * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-07-20 21:31:31 +01:00