- name: trimgalore single-end
  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/trimgalore/test.fastq.gz_trimming_report.txt
    - path: output/trimgalore/test_trimmed.fq.gz

- name: trimgalore paired-end
  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/trimgalore/test_1.fastq.gz_trimming_report.txt
    - path: output/trimgalore/test_1_val_1.fq.gz
    - path: output/trimgalore/test_2.fastq.gz_trimming_report.txt
    - path: output/trimgalore/test_2_val_2.fq.gz