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https://github.com/MillironX/nf-core_modules.git
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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>
27 lines
1.3 KiB
YAML
27 lines
1.3 KiB
YAML
- name: gatk4 variantfiltration test_gatk4_variantfiltration_vcf_input
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command: nextflow run ./tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/variantfiltration/nextflow.config
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tags:
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- gatk4/variantfiltration
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- gatk4
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files:
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- path: output/gatk4/test.filtered.vcf.gz
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contains:
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[
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"BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365",
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]
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- path: output/gatk4/test.filtered.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 variantfiltration test_gatk4_variantfiltration_gz_input
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command: nextflow run ./tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/variantfiltration/nextflow.config
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tags:
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- gatk4/variantfiltration
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- gatk4
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files:
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- path: output/gatk4/test.filtered.vcf.gz
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contains:
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[
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"BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365",
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]
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- path: output/gatk4/test.filtered.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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