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8 commits

Author SHA1 Message Date
Maxime U. Garcia
5b1ce484b9
feat: _idx -> _tbi (#1074) 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2021-11-15 17:49:20 +01:00
Maxime U. Garcia
3b600af50e
feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0

* update md5checksum

* commit all files

* actually checksum was good, but I suspect something fishy with the tests
 2021-11-11 08:58:59 +01:00
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
43c2779258
Fix version commands (#749) 
* 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) 
* 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
GCJMackenzie
1023a98b51
Getpileupsummaries (#689) 
* first commit, added template files for new module

* created getpileupsummaries script, tests and both yml files

* fixed typo in meta.yml

* Update modules/gatk4/getpileupsummaries/meta.yml

changed gz_tbi to gz.tbi as suggested

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2021-09-13 16:04:14 +01:00