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

- name: gatk4 variantfiltration test_gatk4_variantfiltration
  command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration -c tests/config/nextflow.config
  tags:
    - gatk4/variantfiltration
    - gatk4
  files:
    - path: output/gatk4/test.filtered.vcf
      contains:
        - "AC=2;AN=2;DP=1;DP4=0,0,1,0;MQ=60;MQ0F=0;SGB=-0.379885"
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			`- name: gatk4 variantfiltration test_gatk4_variantfiltration`
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml 2021-07-07 09:10:18 +00:00			`command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration -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:`
			`- path: output/gatk4/test.filtered.vcf`
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			`contains:`
			`- "AC=2;AN=2;DP=1;DP4=0,0,1,0;MQ=60;MQ0F=0;SGB=-0.379885"`