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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>
25 lines
1.1 KiB
YAML
25 lines
1.1 KiB
YAML
- name: gatk4 markduplicates test_gatk4_markduplicates_spark
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command: nextflow run tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
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tags:
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- gatk4
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- gatk4/markduplicatesspark
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files:
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- path: output/gatk4/test.bai
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md5sum: e9c125e82553209933883b4fe2b8d7c2
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- path: output/gatk4/test.bam
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md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9
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- path: output/gatk4/test.metrics
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- path: output/gatk4/versions.yml
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- name: gatk4 markduplicates test_gatk4_markduplicates_spark_multiple_bams
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command: nextflow run tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
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tags:
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- gatk4
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- gatk4/markduplicatesspark
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files:
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- path: output/gatk4/test.bai
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md5sum: bad71df9c876e72a5bc0a3e0fd755f92
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- path: output/gatk4/test.bam
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md5sum: 8187febc6108ffef7f907e89b9c091a4
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- path: output/gatk4/test.metrics
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- path: output/gatk4/versions.yml
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