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
Maxime U. Garcia
1abe23e159
Add CRAM to samtools/index ( #1049 )
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* feat: update samtools/index
* feat: add test
* fix: lint
* fix: output file + md5
2021-11-10 10:30:48 +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
Harshil Patel
c5235a983d
nf-core modules bump-versions for all modules ( #630 )
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* Add blacklist of modules that shouldn't be updated to .nf-core.yml
* nf-core modules bump-versions for all modules
* Remove TODO statements identified by linting
* Fix md5sums for failing tests
* Fix more tests
2021-07-28 09:10:44 +01:00
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure ( #567 )
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* Update README
* Rename pytest_software.yml to pytest_modules.yml
* Rename main software directory to modules
* Remove deprecated modules
* Rename tests software to modules
* Replace paths for tests in pytest_modules.yml
* Replace software with modules in Github Actions
* Replace software with modules in main.nf tests
* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00
