- name: gatk4 samtofastq single-end
  command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config
  tags:
    - gatk4
    - gatk4_samtofastq
    - gatk4_samtofastq_single_end
  files:
    - path: ./output/gatk4/test.fastq.gz
      md5sum: 50ace41d4c24467f24f8b929540a7797

- name: gatk4 samtofastq paired-end
  command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config
  tags:
    - gatk4
    - gatk4_samtofastq
    - gatk4_samtofastq_paired_end
  files:
    - path: ./output/gatk4/test_2.fastq.gz
      md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
    - path: ./output/gatk4/test_1.fastq.gz
      md5sum: cfea607c9d75fd9ea9704780ad3a499c