- name: stringtie merge forward-strand
  command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
  tags:
    - stringtie
    - stringtie/merge
  files:
    - path: output/stringtie/stringtie.merged.gtf
      md5sum: d959eb2fab0db48ded7275e0a2e83c05
    - path: output/stringtie/test.ballgown/e2t.ctab
      md5sum: 9ae42e056c955a88a883e5e917840d77
    - path: output/stringtie/test.ballgown/e_data.ctab
      md5sum: adbedee7b2f84c70362ad6dfa57442b7
    - path: output/stringtie/test.ballgown/i2t.ctab
      md5sum: 658131af118cfb416939044fdb5411de
    - path: output/stringtie/test.ballgown/i_data.ctab
      md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
    - path: output/stringtie/test.ballgown/t_data.ctab
      md5sum: 92a98902784e7406ffe054d2adbabc7c
    - path: output/stringtie/test.coverage.gtf
    - path: output/stringtie/test.gene.abundance.txt
      md5sum: 8bcd8e2730ed3337e2730186dbc184f3
    - path: output/stringtie/test.transcripts.gtf
      md5sum: a914bd55b68a4b5f607738b17861e362

- name: stringtie merge test_stringtie_reverse_merge
  command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
  tags:
    - stringtie
    - stringtie/merge
  files:
    - path: output/stringtie/stringtie.merged.gtf
      md5sum: 6da479298d73d5b3216d4e1576a2bdf4
    - path: output/stringtie/test.ballgown/e2t.ctab
      md5sum: 9ae42e056c955a88a883e5e917840d77
    - path: output/stringtie/test.ballgown/e_data.ctab
      md5sum: fd8496d3957ade3b2c0853155f9a67da
    - path: output/stringtie/test.ballgown/i2t.ctab
      md5sum: 658131af118cfb416939044fdb5411de
    - path: output/stringtie/test.ballgown/i_data.ctab
      md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
    - path: output/stringtie/test.ballgown/t_data.ctab
      md5sum: 92a98902784e7406ffe054d2adbabc7c
    - path: output/stringtie/test.coverage.gtf
    - path: output/stringtie/test.gene.abundance.txt
      md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
    - path: output/stringtie/test.transcripts.gtf
      md5sum: 9dcdc9577c0fdbb25089eda210267546

- name: stringtie merge forward-strand stub
  command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config -stub-run
  tags:
    - stringtie
    - stringtie/merge
  files:
    - path: output/stringtie/stringtie.merged.gtf
    - path: output/stringtie/test.coverage.gtf
    - path: output/stringtie/test.gene.abundance.txt
    - path: output/stringtie/test.transcripts.gtf

- name: stringtie merge test_stringtie_reverse_merge stub
  command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config -stub-run
  tags:
    - stringtie
    - stringtie/merge
  files:
    - path: output/stringtie/stringtie.merged.gtf
    - path: output/stringtie/test.coverage.gtf
    - path: output/stringtie/test.gene.abundance.txt
    - path: output/stringtie/test.transcripts.gtf