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
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
a21cc95c69
Add variantbam ( #618 )
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* template created for variantbam (#616 )
* Add bcftools reheader (#585 ) (#608 )
* local tests and linting passing (#585 )
* fix: picard filtersamreads input (#610 )
* Move readlist into same input channel as bam
* Update test reflecting input restructuring
* Update tests/modules/picard/filtersamreads/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix test
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added module arriba (#611 )
* Updated the version of STAR in align and genomegenerate modules
* Changes in test.yml
* Changes in test.yml
* Added module arriba
* Changes in test configs
* Added module Arriba for fusion detection
* Fixed review comments
* Added an output option for discarded fusions
* Resolved some conflits
* conflicts
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* added test for new header
* enhance module fastp: add `save_merged` (#598 ) (#614 )
* enhance module fastp: add `save_merged` (#598 )
* removed md5sum checks from log and json
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
* fixed autogenerated biocontainter links
* variantbam module passing all tests/lints (#616 )
* Added an optional output junction channel in STAR (#621 )
* Added an optional output channel for chimeric junctions
* Fix in test.yml
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* removed qcreport output
fixes #616
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
2021-07-26 19:07:29 +01:00
