- name: Run bismark align single-end test workflow
  command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_single_end -c tests/config/nextflow.config
  tags:
    - bismark
    - bismark/align
  files:
    - path: output/test_single_end/test_methylated_1_bismark_bt2.bam
      md5sum: 7f9744cec5aa7908675e5fae79af36fc
    - path: output/test_single_end/test_methylated_1_bismark_bt2_SE_report.txt

- name: Run bismark align paired-end test workflow
  command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config
  tags:
    - bismark
    - bismark/align
  files:
    - path: output/test_paired_end/test_methylated_1_bismark_bt2_pe.bam
      md5sum: b13d0d40dffd336375f80fc94acc295f
    - path: output/test_paired_end/test_methylated_1_bismark_bt2_PE_report.txt