Commit graph

7 commits

Author SHA1 Message Date
nickhsmith
edfe28a5e0
Variant recalibration (#1885)
* update tests

* update

* update

* make the manta inputs consistant for germline/somatic/tumoronly

* match chromosomes to cram file (chr21)

* undo genotypegvfs

* undo genotypegvfs

* update VariantRecalibrator

* lint

* add '--resource:' tag

Co-authored-by: Smith Nicholas <smith@in.tum.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-07-15 09:21:34 +02:00
Rike
169b2b96c1 update gatk version 2022-05-12 15:45:21 +02:00
Maxime U. Garcia
409af2f27c
Improve syntax/logic coherence in all gatk4 plugins (#1459)
* feat: code polishing

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* code polishing

* more code polishing

* code polishing

* tests for applybqsrspark

* fix typo

* no need to check md5sum for versions.yml

* fix: use correct syntax

* code polishing again

* add tests for markduplicatesspark

* simplify mergevcfs tests

* add tests for baserecalibratorspark

* fix: path to entry

* code polishing

* fix linting

* simplify module

* update meta.yml

* fix pair mode

* fix: MITO mode

* more tests

* fix command

* bad copy paste

* fix typos

* fix tests

* fix test

* update meta.yml

* correct versions.yml in all test.yml

* code polishing

* code polishing

* more code polishing

* fix args

* add tmpdir for all

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 17:15:39 +02:00
FriederikeHanssen
967fb22ded
Update versions (#1292)
* Update versions

* update checksums + remove variables as input for applyvqsr

* sneak in removal of values and provide them via modules.config

* update another checksum

* more checksums

* move vairable to config

* remove controlfreec, wrong branch

* add line break
2022-02-15 11:29:36 +01:00
Mahesh Binzer-Panchal
e20e57f90b
Add when: block (#1261) 2022-02-04 09:53:32 +01:00
FriederikeHanssen
598d7abdb2
Log4j again (#1202)
* Log4j again

* Update checksums
2022-01-12 13:55:54 +01:00
GCJMackenzie
54e0ac4ed9
add module: Variantrecalibrator (#1088)
* committing to pull updated nf-core files

* saving changes to checout other branch

* committing progress so far, difficulty with test data

* uploading to be used as draft PR

* fix linting error in meta.yml

* attempt to group reference inputs together

* updated input format for resources

* meta.yml updated with new resource names

* added output channel for recal index

* module only takes single vcf file input now

* committing to checkout

* update to new syntax, remove indel test for now

* updated to use memory options and new test data

* Update modules/gatk4/variantrecalibrator/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update main.nf

* Update modules/gatk4/variantrecalibrator/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* remove duplicate test keys from test_data.config

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-16 10:54:49 +00:00