- name: damageprofiler test_damageprofiler
  command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config  -c ./tests/modules/damageprofiler/nextflow.config
  tags:
    - damageprofiler
  files:
    - path: output/damageprofiler/test/3pGtoA_freq.txt
      md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
      md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
    - path: output/damageprofiler/test/5pCtoT_freq.txt
      md5sum: 38b5d7c87ec2d8422bc5587095711c5f
    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
      md5sum: 05e041ff47e7c6d08ede51f5c81a2464
    - path: output/damageprofiler/test/DNA_comp_genome.txt
      md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
    - path: output/damageprofiler/test/DNA_composition_sample.txt
      md5sum: 16be9c91a06fa7defee376230b12862f
    - path: output/damageprofiler/test/DamagePlot.pdf
    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
    - path: output/damageprofiler/test/DamageProfiler.log
    - path: output/damageprofiler/test/Length_plot.pdf
    - path: output/damageprofiler/test/Length_plot_combined_data.svg
    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
    - path: output/damageprofiler/test/dmgprof.json
      md5sum: a011a47edaadb3a07527c329a6492570
    - path: output/damageprofiler/test/editDistance.txt
      md5sum: 7590dac007633ee11025cc99ec9f009b
    - path: output/damageprofiler/test/edit_distance.pdf
    - path: output/damageprofiler/test/edit_distance.svg
    - path: output/damageprofiler/test/lgdistribution.txt
      md5sum: 583fd98094de3fb462b133daeaadcf52
    - path: output/damageprofiler/test/misincorporation.txt
      md5sum: 25119c0fcc8839fdbb3ed10922fb07f4

- name: damageprofiler test_damageprofiler_reference
  command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config  -c ./tests/modules/damageprofiler/nextflow.config
  tags:
    - damageprofiler
  files:
    - path: output/damageprofiler/test/3pGtoA_freq.txt
      md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
      md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
    - path: output/damageprofiler/test/5pCtoT_freq.txt
      md5sum: 38b5d7c87ec2d8422bc5587095711c5f
    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
      md5sum: 05e041ff47e7c6d08ede51f5c81a2464
    - path: output/damageprofiler/test/DNA_comp_genome.txt
      md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
    - path: output/damageprofiler/test/DNA_composition_sample.txt
      md5sum: 16be9c91a06fa7defee376230b12862f
    - path: output/damageprofiler/test/DamagePlot.pdf
    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
    - path: output/damageprofiler/test/DamageProfiler.log
    - path: output/damageprofiler/test/Length_plot.pdf
    - path: output/damageprofiler/test/Length_plot_combined_data.svg
    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
    - path: output/damageprofiler/test/dmgprof.json
      md5sum: a011a47edaadb3a07527c329a6492570
    - path: output/damageprofiler/test/editDistance.txt
      md5sum: 7590dac007633ee11025cc99ec9f009b
    - path: output/damageprofiler/test/edit_distance.pdf
    - path: output/damageprofiler/test/edit_distance.svg
    - path: output/damageprofiler/test/lgdistribution.txt
      md5sum: 583fd98094de3fb462b133daeaadcf52
    - path: output/damageprofiler/test/misincorporation.txt
      md5sum: 25119c0fcc8839fdbb3ed10922fb07f4

- name: damageprofiler test_damageprofiler_specieslist
  command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config  -c ./tests/modules/damageprofiler/nextflow.config
  tags:
    - damageprofiler
  files:
    - path: output/damageprofiler/test/DamageProfiler.log
      #contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'