Commit graph

8 commits

Author SHA1 Message Date
Maxime U. Garcia
eb15df8036
Deepvariant - Update main.nf (#2110)
Update main.nf

simplify deepvariant container call
2022-09-27 15:34:10 +02:00
Ramprasad Neethiraj
fd5f6f5f4f
Revert recent changes made to some of the modules (#1463)
* revert changes to modules

* fix tests

* fix kraken2

* fix untar

* fix cat

* add blank lines

* fix typo
2022-03-30 20:21:06 +02:00
Ramprasad Neethiraj
49b18b1639
add stub to modules used in raredisease pipeline (#1206)
* add stub section

* add stub for bcftools norm

* add stub to more modules

* fix expansionhunter tests

* revert changes -picard

* Update stub to write version no.s to a file

* add picard

* revert picard again

* add stubs to more modules

* fix bwamem2

* add bcftools view

* add stubs

* fix svdb query

* review suggestions
2022-03-28 17:48:39 +02:00
FriederikeHanssen
c450b08a75
separate gvcf and vcf in output channels (#1371)
* separate gvcf and vcf in output channels

* regex not working, just using prefix now
2022-03-03 11:54:07 +01:00
Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config (#1279)
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
Mahesh Binzer-Panchal
e20e57f90b
Add when: block (#1261) 2022-02-04 09:53:32 +01:00
FriederikeHanssen
1287ba48fe
Update version & add intervals usage (#1214)
* Update version & add intervals usage

* Fix config when passing intervals as file

* Use proper paths
2022-01-17 16:40:31 +01:00
Abhinav Sharma
6243c3792c
module: deepvariant (#572)
* Add stubs for deepvariant [ci skip]

* Update the stubs for deepvariant [ci skip]

* functional with google docker image

* cleanup

* consume docker container within singularity executor

* update the meta.yml file and ask for review

* tweak the input channel shape and test data

* tweak input data [ci skip]

* update for the new syntax

* remove the functions and rename meta vars

* Update the arguments mechanism

* update chr, region and checksum

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-01-17 12:25:36 +02:00