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9 commits

Author SHA1 Message Date
Kevin
3aacd46da2
Backfill software licenses meta (#876) 
* 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) 
* 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
9c31cf1566
Fix version commands: round 3 (#754) 
* Fix version commands: round 3

* Fix seqkit/split2 modules
 2021-09-28 14:37:47 +01:00
Gregor Sturm
906577873b
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>
 2021-09-27 09:41:24 +01:00
praveenraj2018
5de3f2c50e
Added PL tag in read group information for downstream analysis (#649) 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2021-08-04 11:16:51 +02:00
praveenraj2018
df909015b6
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>
 2021-07-26 19:03:30 +02:00
praveenraj2018
f43778b0e6
Updated the version of STAR in align and genomegenerate modules (#604) 
* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-21 13:30:52 +01:00
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567) 
* 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