FriederikeHanssen
19035c99d1
Add thread option to samtools modules ( #1069 )
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* 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
Kevin
3aacd46da2
Backfill software licenses meta ( #876 )
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* backfilled modules with meta.yml that had no license identifier
* harmonized BSD license names
* whitespace linting at modules/unzip/meta.yml:12
* harmonized software from US NIH-NCBI/NIST to 'US-Government-Work'
* Update modules/bcftools/index/meta.yml
`bcftools` is dual-licensed, use associative array to allow for multiple licenses
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Michael L Heuer <heuermh@acm.org>
2021-10-22 15:39:54 -07:00
Harshil Patel
49da864287
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
Harshil Patel
7b3315591a
Remove def software lines and emit versions channel as plural ( #780 )
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* Remove def software line
* Replace version with versions in emit statement
* Fix default software names
2021-10-01 14:04:56 +01:00
Harshil Patel
43c2779258
Fix version commands ( #749 )
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* Fix version commands
* Fix version commands: again
2021-09-27 22:10:37 +01:00
Gregor Sturm
906577873b
Bulk update modules to use versions.yml ( #739 )
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* New functions.nf
* Convert code to create versions.yml
* Update meta.yml
* update output channel
* Fix more meta.yml
* Manually update remaining modules
* remove superflous echo
* Fix misformatted meta.yml files
* Fix yaml, was list instead of dict
* fix version for bcftools
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 09:41:24 +01:00
Johnathan D
2e619add87
Add samtools ampliconclip ( #590 )
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* 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
