- name: bbmap bbduk test_bbmap_bbduk_single_end
  command: nextflow run tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_single_end -c tests/config/nextflow.config
  tags:
    - bbmap/bbduk
  files:
    - path: output/bbmap/test.trim.bbduk.log
      contains:
        - "Input is being processed as unpaired"
    - path: output/bbmap/test.trim.fastq.gz
      md5sum: a87d0cbd5ced7df8bf1751e4cb407482

- name: bbmap bbduk test_bbmap_bbduk_paired_end
  command: nextflow run tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_paired_end -c tests/config/nextflow.config
  tags:
    - bbmap/bbduk
  files:
    - path: output/bbmap/test.trim.bbduk.log
      contains:
        - "Input is being processed as paired"
    - path: output/bbmap/test.trim_1.fastq.gz
      md5sum: a87d0cbd5ced7df8bf1751e4cb407482
    - path: output/bbmap/test.trim_2.fastq.gz
      md5sum: 406e068fbe198f02b48e7e210cc0c69f

- name: bbmap bbduk test_bbmap_bbduk_se_ref
  command: nextflow run tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_se_ref -c tests/config/nextflow.config
  tags:
    - bbmap/bbduk
  files:
    - path: output/bbmap/test.trim.bbduk.log
      contains:
        - "Input is being processed as unpaired"
    - path: output/bbmap/test.trim.fastq.gz
      md5sum: 3970e82605c7d109bb348fc94e9eecc0

- name: bbmap bbduk test_bbmap_bbduk_pe_ref
  command: nextflow run tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_pe_ref -c tests/config/nextflow.config
  tags:
    - bbmap/bbduk
  files:
    - path: output/bbmap/test.trim.bbduk.log
      contains:
        - "Input is being processed as paired"
    - path: output/bbmap/test.trim_1.fastq.gz
      md5sum: 3970e82605c7d109bb348fc94e9eecc0
    - path: output/bbmap/test.trim_2.fastq.gz
      md5sum: 3970e82605c7d109bb348fc94e9eecc0