- 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/bowtie/NC_010473.1.ebwt
      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
    - path: output/bowtie/bowtie/NC_010473.2.ebwt
      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
    - path: output/bowtie/bowtie/NC_010473.3.ebwt
      md5sum: cd201e81724f3099131aec16ef2cc53b
    - path: output/bowtie/bowtie/NC_010473.4.ebwt
      md5sum: bbb9d6d21ad765d135f95290204e8433
    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
      md5sum: 44f719c2fe42e1f35d54e798775846d1
    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
      md5sum: f3c398bba5158f4039334a932d79c051

- name: Run bowtie index and align single-end
  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
  tags:
    - bowtie
    - bowtie_align
  files:
    - path: output/bowtie/bowtie/NC_010473.1.ebwt
      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
    - path: output/bowtie/bowtie/NC_010473.2.ebwt
      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
    - path: output/bowtie/bowtie/NC_010473.3.ebwt
      md5sum: cd201e81724f3099131aec16ef2cc53b
    - path: output/bowtie/bowtie/NC_010473.4.ebwt
      md5sum: bbb9d6d21ad765d135f95290204e8433
    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
      md5sum: 44f719c2fe42e1f35d54e798775846d1
    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
      md5sum: f3c398bba5158f4039334a932d79c051
    - path: output/bowtie/test.out
      md5sum: a81cb18024616415a6cec3108a36fccd
    - path: output/bowtie/test.bam
      md5sum: 9feed8a55d4b5e600dcc577768ef07fc

- name: Run bowtie index and align paired-end
  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
  tags:
    - bowtie
    - bowtie_align
  files:
    - path: output/bowtie/bowtie/NC_010473.1.ebwt
      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
    - path: output/bowtie/bowtie/NC_010473.2.ebwt
      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
    - path: output/bowtie/bowtie/NC_010473.3.ebwt
      md5sum: cd201e81724f3099131aec16ef2cc53b
    - path: output/bowtie/bowtie/NC_010473.4.ebwt
      md5sum: bbb9d6d21ad765d135f95290204e8433
    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
      md5sum: 44f719c2fe42e1f35d54e798775846d1
    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
      md5sum: f3c398bba5158f4039334a932d79c051
    - path: output/bowtie/test.out
      md5sum: a23e9a2a76e949aeb3693bcfae41a615
    - path: output/bowtie/test.bam
      md5sum: cf6a6381aa504e8342638ff3b509721e