- name: Run trimgalore single-end test workflow
  command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_single_end -c tests/config/nextflow.config
  tags:
    - trimgalore
  files:
    # These can't be md5'd reliably
    # TODO Test for includes
    - path: output/test_single_end/test.fastq.gz_trimming_report.txt
    - path: output/test_single_end/test_trimmed.fq.gz

- name: Run trimgalore paired-end test workflow
  command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_paired_end -c tests/config/nextflow.config
  tags:
    - trimgalore
  files:
    # These can't be md5'd reliably
    # TODO Test for includes
    - path: output/test_paired_end/test_1.fastq.gz_trimming_report.txt
    - path: output/test_paired_end/test_1_val_1.fq.gz
    - path: output/test_paired_end/test_2.fastq.gz_trimming_report.txt
    - path: output/test_paired_end/test_2_val_2.fq.gz