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

- name: gatk4 variantfiltration test_gatk4_variantfiltration_vcf_input
  command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_vcf_input -c tests/config/nextflow.config
  tags:
    - gatk4/variantfiltration
    - gatk4
  files:
    - path: output/gatk4/test.filtered.vcf.gz
      contains: ['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']
    - path: output/gatk4/test.filtered.vcf.gz.tbi

- name: gatk4 variantfiltration test_gatk4_variantfiltration_gz_input
  command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_gz_input -c tests/config/nextflow.config
  tags:
    - gatk4/variantfiltration
    - gatk4
  files:
    - path: output/gatk4/test.filtered.vcf.gz
      contains: ['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']
    - path: output/gatk4/test.filtered.vcf.gz.tbi
Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083) * Added vcf_index to vcf tuple; output to vcf.gz format. * Fix: extra new line in meta.yml. * addressed review feedback * fix: editorconfig error * fix: gatk memory flag * fix: editorconfig error * fix: Indentation fix: Indentation * Fix: lint editorconfig error Removed one extra space Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> 2021-11-18 20:47:40 +00:00			`- name: gatk4 variantfiltration test_gatk4_variantfiltration_vcf_input`
			`command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_vcf_input -c tests/config/nextflow.config`
added gatk4 variantfiltration (#265) * added gatk4 variantfiltration * replace merge with filter * Update software/gatk4/variantfiltration/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * updated input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2021-03-17 08:42:35 +00:00			`tags:`
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2021-04-08 08:10:52 +00:00			`- gatk4/variantfiltration`
update test data paths (#373) * update test data paths * Update test md5sums * gatk test fixes & update variantfiltration main * few extra fixes after review * fix suspected format error * Update software/gatk4/variantfiltration/main.nf * Update software/gatk4/variantfiltration/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2021-03-24 18:14:11 +00:00			`- gatk4`
added gatk4 variantfiltration (#265) * added gatk4 variantfiltration * replace merge with filter * Update software/gatk4/variantfiltration/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * updated input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2021-03-17 08:42:35 +00:00			`files:`
Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083) * Added vcf_index to vcf tuple; output to vcf.gz format. * Fix: extra new line in meta.yml. * addressed review feedback * fix: editorconfig error * fix: gatk memory flag * fix: editorconfig error * fix: Indentation fix: Indentation * Fix: lint editorconfig error Removed one extra space Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> 2021-11-18 20:47:40 +00:00			`- path: output/gatk4/test.filtered.vcf.gz`
			`contains: ['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']`
			`- path: output/gatk4/test.filtered.vcf.gz.tbi`

			`- name: gatk4 variantfiltration test_gatk4_variantfiltration_gz_input`
			`command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_gz_input -c tests/config/nextflow.config`
			`tags:`
			`- gatk4/variantfiltration`
			`- gatk4`
			`files:`
			`- path: output/gatk4/test.filtered.vcf.gz`
			`contains: ['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']`
			`- path: output/gatk4/test.filtered.vcf.gz.tbi`