- 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: 61c6d3556ac6e0d09d800415b9a48508

- 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_1.fastq.gz
      md5sum: 61c6d3556ac6e0d09d800415b9a48508
    - path: output/gatk4/test_2.fastq.gz
      md5sum: d0e74ab8dccca91c0ccd7125e588d5cd