- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_interval
  command: nextflow run ./tests/modules/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_interval -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/leftalignandtrimvariants/nextflow.config
  tags:
    - gatk4
    - gatk4/leftalignandtrimvariants
  files:
    - path: output/gatk4/test.normalised.vcf.gz
      contains:
        - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
    - path: output/gatk4/test.normalised.vcf.gz.tbi

- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_no_interval
  command: nextflow run ./tests/modules/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_no_interval -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/leftalignandtrimvariants/nextflow.config
  tags:
    - gatk4
    - gatk4/leftalignandtrimvariants
  files:
    - path: output/gatk4/test.normalised.vcf.gz
      contains:
        - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
        - "MT192765.1\t10502\t.\tTAGATTATGACTGTGTCTCTTTTTGTTACATGCACCA\tTAGAT"
    - path: output/gatk4/test.normalised.vcf.gz.tbi