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9f8d9fb615
* initial commit to setup branch * workflow finished * Update nextflow.config * tumour to tumor, getpileup passed as nomral and tumor * paired_somatic renamed to tumor_normal_somatic * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * updated index names in meta.yml * changed index file names in main script and test * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Apply suggestions from code review * fixed bug from changes * Apply suggestions from code review * modified yml to allow new subworkflow testing * Update test.yml * Update test.yml * add applyvqsr * added memory options, new test data used * Update main.nf * Update main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
17 lines
711 B
YAML
17 lines
711 B
YAML
- name: gatk4 applyvqsr test_gatk4_applyvqsr
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command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
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tags:
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- gatk4
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- gatk4/applyvqsr
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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.tbi
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- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific
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command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
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tags:
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- gatk4
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- gatk4/applyvqsr
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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.tbi
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