- name: gatk4 samtofastq test_gatk4_samtofastq_single_end
  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config
  tags:
    - gatk4
    - gatk4/samtofastq
  files:
    - path: output/gatk4/test.fastq.gz
      md5sum: 50ace41d4c24467f24f8b929540a7797
    - path: output/gatk4/versions.yml

- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end
  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config
  tags:
    - gatk4
    - gatk4/samtofastq
  files:
    - path: output/gatk4/test_1.fastq.gz
      md5sum: cfea607c9d75fd9ea9704780ad3a499c
    - path: output/gatk4/test_2.fastq.gz
      md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
    - path: output/gatk4/versions.yml

- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
  tags:
    - gatk4
    - gatk4/samtofastq
  files:
    - path: output/gatk4/test_1.fastq.gz
    - path: output/gatk4/test_2.fastq.gz
    - path: output/gatk4/versions.yml