- name: Run bowtie index
  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config
  tags:
    - bowtie
    - bowtie_index
  files:
    - path: output/bowtie/NC_010473.index.1.ebwt
      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
    - path: output/bowtie/NC_010473.index.2.ebwt
      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
    - path: output/bowtie/NC_010473.index.3.ebwt
      md5sum: cd201e81724f3099131aec16ef2cc53b
    - path: output/bowtie/NC_010473.index.4.ebwt
      md5sum: bbb9d6d21ad765d135f95290204e8433
    - path: output/bowtie/NC_010473.index.rev.1.ebwt
      md5sum: 44f719c2fe42e1f35d54e798775846d1
    - path: output/bowtie/NC_010473.index.rev.2.ebwt
      md5sum: f3c398bba5158f4039334a932d79c051

- name: Run bowtie index and align signle-end
  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
  tags:
    - bowtie
    - bwa_align
  files:
    - path: output/bowtie/NC_010473.index.1.ebwt
      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
    - path: output/bowtie/NC_010473.index.2.ebwt
      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
    - path: output/bowtie/NC_010473.index.3.ebwt
      md5sum: cd201e81724f3099131aec16ef2cc53b
    - path: output/bowtie/NC_010473.index.4.ebwt
      md5sum: bbb9d6d21ad765d135f95290204e8433
    - path: output/bowtie/NC_010473.index.rev.1.ebwt
      md5sum: 44f719c2fe42e1f35d54e798775846d1
    - path: output/bowtie/NC_010473.index.rev.2.ebwt
      md5sum: f3c398bba5158f4039334a932d79c051
    - path: output/bowtie/test.out
      md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
    - path: output/bowtie/test.sam
      md5sum: acdb36ea915ac2ac71b69a0b704d9d8a