nf-core_modules/tests/modules/gatk4/combinegvcfs/test.yml at 919275103a00ddbcfc31b2c424837efaaf2ef0a8 - millironx/nf-core_modules - Milliron X Code: Code hosting for cattle or technology, but especially anything to do with both of them

millironx/nf-core_modules

mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-11 04:33:10 +00:00

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

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YAML

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 - name: gatk4 combinegvcfs test_gatk4_combinegvcfs
   command: nextflow run tests/modules/gatk4/combinegvcfs -entry test_gatk4_combinegvcfs -c tests/config/nextflow.config
   tags:
     - gatk4
     - gatk4/combinegvcfs
   files:
     - path: output/gatk4/test.combined.g.vcf.gz
       contains: ["VCFv4.2"]
     - path: output/gatk4/versions.yml