- name: trimmomatic single-end
  command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_single_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
  tags:
    - "trimmomatic"
  files:
    - path: "output/trimmomatic/test.SE.paired.trim.fastq.gz"
    - path: "output/trimmomatic/test.log"
      md5sum: e4c3f619e9b0e26847f8f3e3d9af319b

- name: trimmomatic paired-end
  command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
  tags:
    - "trimmomatic"
  files:
    - path: "output/trimmomatic/test.log"
      md5sum: 9629761761a34576b3484bf4174f681f
    - path: "output/trimmomatic/test.paired.trim_1.fastq.gz"
    - path: "output/trimmomatic/test.unpaired.trim_1.fastq.gz"
    - path: "output/trimmomatic/test.paired.trim_2.fastq.gz"
    - path: "output/trimmomatic/test.unpaired.trim_2.fastq.gz"

- name: trimmomatic no adapter specified
  command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_no_adaptor -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
  tags:
    - "trimmomatic"
  exit_code: 1