mirror of
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>
71 lines
2.9 KiB
YAML
71 lines
2.9 KiB
YAML
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair
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command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
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tags:
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- gatk4
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- gatk4/mutect2
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.stats
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md5sum: 17d2091015d04cbd4a26b7a67dc659e6
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- path: output/gatk4/test.vcf.gz.tbi
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- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2
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command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
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tags:
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- gatk4
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- gatk4/mutect2
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files:
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- path: output/gatk4/test.f1r2.tar.gz
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.stats
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md5sum: 17d2091015d04cbd4a26b7a67dc659e6
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
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command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
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tags:
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- gatk4
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- gatk4/mutect2
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.stats
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md5sum: 55ed641e16089afb33cdbc478e202d3d
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 mutect2 test_gatk4_mutect2_cram_input
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command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_cram_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
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tags:
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- gatk4
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- gatk4/mutect2
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.stats
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md5sum: 55ed641e16089afb33cdbc478e202d3d
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
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command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_generate_pon -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
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tags:
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- gatk4
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- gatk4/mutect2
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.stats
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md5sum: b569ce66bbffe9588b3d221e821023ee
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 mutect2 test_gatk4_mutect2_mitochondria
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command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_mitochondria -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
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tags:
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- gatk4
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- gatk4/mutect2
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.stats
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md5sum: fc6ea14ca2da346babe78161beea28c9
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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