nf-core_modules/tests/modules/gatk4/markduplicates/test.yml
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

25 lines
1.1 KiB
YAML

- name: gatk4 markduplicates test_gatk4_markduplicates
command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
tags:
- gatk4
- gatk4/markduplicates
files:
- path: output/gatk4/test.bai
md5sum: e9c125e82553209933883b4fe2b8d7c2
- path: output/gatk4/test.bam
md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9
- path: output/gatk4/test.metrics
- path: output/gatk4/versions.yml
- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
tags:
- gatk4
- gatk4/markduplicates
files:
- path: output/gatk4/test.bai
md5sum: bad71df9c876e72a5bc0a3e0fd755f92
- path: output/gatk4/test.bam
md5sum: 8187febc6108ffef7f907e89b9c091a4
- path: output/gatk4/test.metrics
- path: output/gatk4/versions.yml