Commit graph

5 commits

Author SHA1 Message Date
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
James A. Fellows Yates
e971f538a9
Module new version reporting fixes (#753)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Fix IQ tree

* Fix picard markdup and merge sam

* Fix plink/vcf version

* Fix plink version output

* Fix prokka version command

* Fix pydamage

* Try fixing markduplicates

* Fix snpEff

* Fix vcftools version

* Fix pydamage and filtersamreads test run

* Fix MarkDuplicates tests

* Add missing unsorted checks

* Remove MD5 sym due to stochasicity in BAM file
2021-09-28 10:51:19 +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
Maxime Borry
d9dfbe9d9d
Add pydamage analyze module (#705)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* simplify PR to analyze subcommand

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 14:03:51 +02:00