- 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 -c ./tests/modules/gatk4/variantfiltration/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
    - path: output/gatk4/versions.yml

- 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 -c ./tests/modules/gatk4/variantfiltration/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
    - path: output/gatk4/versions.yml