- name: salmon quant single-end
  command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_single_end -c tests/config/nextflow.config
  tags:
    - salmon
    - salmon/quant
  files:
    - path: ./output/salmon/test/cmd_info.json
    - path: ./output/salmon/test/quant.sf
      md5sum: 687368b9963874c1797d210310b38516
    - path: ./output/salmon/test/lib_format_counts.json
    - path: ./output/salmon/test/quant.genes.sf
      md5sum: ad4d31437f06db49b2436abeec29c78e
    - path: ./output/salmon/test/logs/salmon_quant.log
    - path: ./output/salmon/test/aux_info/expected_bias.gz
      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
    - path: ./output/salmon/test/aux_info/observed_bias_3p.gz
      md5sum: ef13c06a538e9c34ca9f84212c82f44e
    - path: ./output/salmon/test/aux_info/meta_info.json
    - path: ./output/salmon/test/aux_info/fld.gz
    - path: ./output/salmon/test/aux_info/ambig_info.tsv
      md5sum: 2ee3dc3080ad7222e0687481e7a1ee03
    - path: ./output/salmon/test/aux_info/observed_bias.gz
      md5sum: ef13c06a538e9c34ca9f84212c82f44e
    - path: ./output/salmon/test/libParams/flenDist.txt
      md5sum: 2de170bdc9f6fd237d286429b292bb28
    - path: ./output/index/salmon/ref_indexing.log
    - path: ./output/index/salmon/refseq.bin
      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
    - path: ./output/index/salmon/versionInfo.json
      md5sum: 204865f645102587c4953fccb256797c
    - path: ./output/index/salmon/complete_ref_lens.bin
      md5sum: f57562f1fca3ae7b133f895ae13c3d08
    - path: ./output/index/salmon/mphf.bin
      md5sum: 53669a47610e33e031faafd32703b714
    - path: ./output/index/salmon/pre_indexing.log
    - path: ./output/index/salmon/ctable.bin
    - path: ./output/index/salmon/duplicate_clusters.tsv
      md5sum: 51b5292e3a874119c0e1aa566e95d70c
    - path: ./output/index/salmon/reflengths.bin
      md5sum: f57562f1fca3ae7b133f895ae13c3d08
    - path: ./output/index/salmon/info.json
      md5sum: 61ff4d3471134c280668355ddd39e99f
    - path: ./output/index/salmon/refAccumLengths.bin
      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
    - path: ./output/index/salmon/ctg_offsets.bin
      md5sum: 27a76542337df436436e66017f66dd25
    - path: ./output/index/salmon/rank.bin
      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
    - path: ./output/index/salmon/pos.bin
    - path: ./output/index/salmon/seq.bin

- name: salmon quant paired end
  command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
  tags:
    - salmon
    - salmon/quant
  files:
    - path: ./output/salmon/test/cmd_info.json
    - path: ./output/salmon/test/quant.sf
      md5sum: 4abd35d0a60b5279b394424f0e6ea42d
    - path: ./output/salmon/test/lib_format_counts.json
    - path: ./output/salmon/test/quant.genes.sf
      md5sum: d750f8c9f248e30c3a6d0c2678bf9c6a
    - path: ./output/salmon/test/logs/salmon_quant.log
    - path: ./output/salmon/test/aux_info/expected_bias.gz
      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
    - path: ./output/salmon/test/aux_info/observed_bias_3p.gz
      md5sum: ef13c06a538e9c34ca9f84212c82f44e
    - path: ./output/salmon/test/aux_info/meta_info.json
    - path: ./output/salmon/test/aux_info/fld.gz
    - path: ./output/salmon/test/aux_info/ambig_info.tsv
      md5sum: 33c0df069da554344869604ea8c18b22
    - path: ./output/salmon/test/aux_info/observed_bias.gz
      md5sum: ef13c06a538e9c34ca9f84212c82f44e
    - path: ./output/salmon/test/libParams/flenDist.txt
      md5sum: 221f754ed55dd1e34874f9b7b3f9d240
    - path: ./output/index/salmon/ref_indexing.log
    - path: ./output/index/salmon/refseq.bin
      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
    - path: ./output/index/salmon/versionInfo.json
      md5sum: 204865f645102587c4953fccb256797c
    - path: ./output/index/salmon/complete_ref_lens.bin
      md5sum: f57562f1fca3ae7b133f895ae13c3d08
    - path: ./output/index/salmon/mphf.bin
      md5sum: 53669a47610e33e031faafd32703b714
    - path: ./output/index/salmon/pre_indexing.log
    - path: ./output/index/salmon/ctable.bin
    - path: ./output/index/salmon/duplicate_clusters.tsv
      md5sum: 51b5292e3a874119c0e1aa566e95d70c
    - path: ./output/index/salmon/reflengths.bin
      md5sum: f57562f1fca3ae7b133f895ae13c3d08
    - path: ./output/index/salmon/info.json
      md5sum: 61ff4d3471134c280668355ddd39e99f
    - path: ./output/index/salmon/refAccumLengths.bin
      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
    - path: ./output/index/salmon/ctg_offsets.bin
      md5sum: 27a76542337df436436e66017f66dd25

    - path: ./output/index/salmon/rank.bin
      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
    - path: ./output/index/salmon/pos.bin
    - path: ./output/index/salmon/seq.bin

- name: salmon quant test_salmon_quant_single_end_lib_type_A
  command: nextflow run tests/modules/salmon/quant -entry test_salmon_quant_single_end_lib_type_A -c tests/config/nextflow.config
  tags:
    - salmon/quant
    - salmon
  files:
    - path: ./output/salmon/test/cmd_info.json
    - path: output/salmon/test/quant.sf
      md5sum: 687368b9963874c1797d210310b38516
    - path: ./output/salmon/test/lib_format_counts.json
    - path: ./output/salmon/test/quant.genes.sf
      md5sum: ad4d31437f06db49b2436abeec29c78e
    - path: ./output/salmon/test/logs/salmon_quant.log
    - path: output/salmon/test/aux_info/expected_bias.gz
      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
    - path: output/salmon/test/aux_info/observed_bias_3p.gz
      md5sum: ef13c06a538e9c34ca9f84212c82f44e
    - path: ./output/salmon/test/aux_info/meta_info.json
    - path: ./output/salmon/test/aux_info/fld.gz
    - path: output/salmon/test/aux_info/ambig_info.tsv
      md5sum: 2ee3dc3080ad7222e0687481e7a1ee03
    - path: ./output/salmon/test/aux_info/observed_bias.gz
      md5sum: ef13c06a538e9c34ca9f84212c82f44e
    - path: output/salmon/test/libParams/flenDist.txt
      md5sum: 2de170bdc9f6fd237d286429b292bb28
    - path: ./output/index/salmon/ref_indexing.log
    - path: output/index/salmon/refseq.bin
      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
    - path: output/index/salmon/versionInfo.json
      md5sum: 204865f645102587c4953fccb256797c
    - path: output/index/salmon/complete_ref_lens.bin
      md5sum: f57562f1fca3ae7b133f895ae13c3d08
    - path: output/index/salmon/mphf.bin
      md5sum: 53669a47610e33e031faafd32703b714
    - path: output/index/salmon/duplicate_clusters.tsv
      md5sum: 51b5292e3a874119c0e1aa566e95d70c
    - path: output/index/salmon/reflengths.bin
      md5sum: f57562f1fca3ae7b133f895ae13c3d08
    - path: output/index/salmon/info.json
      md5sum: 61ff4d3471134c280668355ddd39e99f
    - path: output/index/salmon/refAccumLengths.bin
      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
    - path: output/index/salmon/ctg_offsets.bin
      md5sum: 27a76542337df436436e66017f66dd25
    - path: output/index/salmon/rank.bin
      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
    - path: ./output/index/salmon/pos.bin
    - path: ./output/index/salmon/seq.bin