nf-core_modules/tests/modules/gatk4/applyvqsr/test.yml

- name: gatk4 applyvqsr test_gatk4_applyvqsr
  command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
  tags:
    - gatk4
    - gatk4/applyvqsr
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.tbi

- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific
  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
  tags:
    - gatk4
    - gatk4/applyvqsr
  files:
    - path: output/gatk4/test.vcf.gz
    - path: output/gatk4/test.vcf.gz.tbi
Add applyvqsr (#1101) * 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> 2021-12-16 08:44:50 +00:00			`- name: gatk4 applyvqsr test_gatk4_applyvqsr`
			`command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config`
			`tags:`
			`- gatk4`
			`- gatk4/applyvqsr`
			`files:`
			`- path: output/gatk4/test.vcf.gz`
			`- path: output/gatk4/test.vcf.gz.tbi`

			`- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific`
			`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`
			`tags:`
			`- gatk4`
			`- gatk4/applyvqsr`
			`files:`
			`- path: output/gatk4/test.vcf.gz`
			`- path: output/gatk4/test.vcf.gz.tbi`