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409af2f27c
* 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>
21 lines
925 B
YAML
21 lines
925 B
YAML
- name: gatk4 samtofastq test_gatk4_samtofastq_single_end
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command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config
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tags:
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- gatk4
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- gatk4/samtofastq
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files:
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- path: output/gatk4/test.fastq.gz
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md5sum: 50ace41d4c24467f24f8b929540a7797
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- path: output/gatk4/versions.yml
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- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end
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command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config
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tags:
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- gatk4
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- gatk4/samtofastq
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files:
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- path: output/gatk4/test_1.fastq.gz
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md5sum: cfea607c9d75fd9ea9704780ad3a499c
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- path: output/gatk4/test_2.fastq.gz
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md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
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- path: output/gatk4/versions.yml
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