- name: Run bowtie2 build
  command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_build -c tests/config/nextflow.config
  tags:
    - bowtie2
    - bowtie2_build
  files:
    - path: output/bowtie2/bowtie2/NC_010473.1.bt2
      md5sum: 4db22d92e72111a5fbf609b3d9a43015
    - path: output/bowtie2/bowtie2/NC_010473.2.bt2
      md5sum: f4429ec74ee0064732c4bb26718a3eb1
    - path: output/bowtie2/bowtie2/NC_010473.3.bt2
      md5sum: cd201e81724f3099131aec16ef2cc53b
    - path: output/bowtie2/bowtie2/NC_010473.4.bt2
      md5sum: bbb9d6d21ad765d135f95290204e8433
    - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
      md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
    - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72

- name: Run bowtie2 index and align single-end
  command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config
  tags:
    - bowtie2
    - bowtie2_align
  files:
    - path: output/bowtie2/bowtie2/NC_010473.1.bt2
      md5sum: 4db22d92e72111a5fbf609b3d9a43015
    - path: output/bowtie2/bowtie2/NC_010473.2.bt2
      md5sum: f4429ec74ee0064732c4bb26718a3eb1
    - path: output/bowtie2/bowtie2/NC_010473.3.bt2
      md5sum: cd201e81724f3099131aec16ef2cc53b
    - path: output/bowtie2/bowtie2/NC_010473.4.bt2
      md5sum: bbb9d6d21ad765d135f95290204e8433
    - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
      md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
    - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
    - path: output/bowtie2/test.bowtie2.log
      md5sum: 90041c264231be535042adb93a279356
    - path: output/bowtie2/test.bam
      md5sum: 906102f401d8234b6473790988fb09cf

- name: Run bowtie2 index and align paired-end
  command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config
  tags:
    - bowtie2
    - bowtie2_align
  files:
    - path: output/bowtie2/bowtie2/NC_010473.1.bt2
      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
    - path: output/bowtie2/bowtie2/NC_010473.2.bt2
      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
    - path: output/bowtie2/bowtie2/NC_010473.3.bt2
      md5sum: cd201e81724f3099131aec16ef2cc53b
    - path: output/bowtie2/bowtie2/NC_010473.4.bt2
      md5sum: bbb9d6d21ad765d135f95290204e8433
    - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
      md5sum: 44f719c2fe42e1f35d54e798775846d1
    - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
      md5sum: f3c398bba5158f4039334a932d79c051
    - path: output/bowtie2/test.bowtie2.log
      md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5
    - path: output/bowtie2/test.bam
      md5sum: 732a33cd9816b38ea9b919c25eeb78f8