FriederikeHanssen
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19035c99d1
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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>
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2021-11-18 22:24:47 +01:00 |
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Harshil Patel
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7b3315591a
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Remove def software lines and emit versions channel as plural (#780)
* Remove def software line
* Replace version with versions in emit statement
* Fix default software names
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2021-10-01 14:04:56 +01:00 |
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Harshil Patel
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43c2779258
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Fix version commands (#749)
* Fix version commands
* Fix version commands: again
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2021-09-27 22:10:37 +01:00 |
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Gregor Sturm
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906577873b
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Bulk update modules to use versions.yml (#739)
* 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>
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2021-09-27 09:41:24 +01:00 |
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Johnathan D
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2e619add87
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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>
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2021-07-20 21:31:31 +01:00 |
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