- name: bbmap align paired end fasta ref
  command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_fasta_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
  tags:
    - bbmap
    - bbmap/align
  files:
    - path: output/bbmap/test.bam
      md5sum: 8549040067d23949bddb6fe2ad211c92
    - path: output/bbmap/test.bbmap.log

- name: bbmap align paired end index ref
  command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
  tags:
    - bbmap
    - bbmap/align
  files:
    - path: output/bbmap/test.bam
      md5sum: aeb842491ca6c7806aa7103b5223620f
    - path: output/bbmap/test.bbmap.log

- name: bbmap align single end index ref
  command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_single_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
  tags:
    - bbmap
    - bbmap/align
  files:
    - path: output/bbmap/test.bam
      md5sum: b6a41cb344a343d46244d8f94eb66ec0
    - path: output/bbmap/test.bbmap.log

- name: bbmap align paired end index ref pigz
  command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
  tags:
    - bbmap
    - bbmap/align
  files:
    - path: output/bbmap/test.bam
      md5sum: 74944e24acccb8c5abc316dcdd623c84
    - path: output/bbmap/test.bbmap.log