- name: damageprofiler
  command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
  tags:
    - damageprofiler
  files:
    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
      md5sum: de3b84d946a6b63cdcfadf82bf6854c0
    - path: output/damageprofiler/test/3pGtoA_freq.txt
      md5sum: 61c903b1504ed7d7182570dfc75e4498
    - path: output/damageprofiler/test/5pCtoT_freq.txt
      md5sum: 15a75b60ee519b61ce04a83fe3afe855
    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
      md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
    - path: output/damageprofiler/test/DamagePlot.pdf
    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
    - path: output/damageprofiler/test/DamageProfiler.log
      contains:
        - "FINISHED SUCCESSFULLY"
    - path: output/damageprofiler/test/dmgprof.json
      md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
    - path: output/damageprofiler/test/DNA_comp_genome.txt
      md5sum: fea48af1ecf491b439d36d4a919473df
    - path: output/damageprofiler/test/DNA_composition_sample.txt
      md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
    - path: output/damageprofiler/test/edit_distance.pdf
    - path: output/damageprofiler/test/edit_distance.svg
    - path: output/damageprofiler/test/editDistance.txt
      md5sum: 04d14b449a5afa8b5dbff0dfa762356b
    - path: output/damageprofiler/test/Length_plot_combined_data.svg
    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
    - path: output/damageprofiler/test/Length_plot.pdf
    - path: output/damageprofiler/test/lgdistribution.txt
      md5sum: df2e19195185ea9ee05e8e84b2948f36
    - path: output/damageprofiler/test/misincorporation.txt
      md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c

- name: damageprofiler_reference
  command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
  tags:
    - damageprofiler
  files:
    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
      md5sum: de3b84d946a6b63cdcfadf82bf6854c0
    - path: output/damageprofiler/test/3pGtoA_freq.txt
      md5sum: 61c903b1504ed7d7182570dfc75e4498
    - path: output/damageprofiler/test/5pCtoT_freq.txt
      md5sum: 15a75b60ee519b61ce04a83fe3afe855
    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
      md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
    - path: output/damageprofiler/test/DamagePlot.pdf
    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
    - path: output/damageprofiler/test/DamageProfiler.log
      contains:
        - "FINISHED SUCCESSFULLY"
    - path: output/damageprofiler/test/dmgprof.json
      md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
    - path: output/damageprofiler/test/DNA_comp_genome.txt
      md5sum: fea48af1ecf491b439d36d4a919473df
    - path: output/damageprofiler/test/DNA_composition_sample.txt
      md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
    - path: output/damageprofiler/test/edit_distance.pdf
    - path: output/damageprofiler/test/edit_distance.svg
    - path: output/damageprofiler/test/editDistance.txt
      md5sum: 04d14b449a5afa8b5dbff0dfa762356b
    - path: output/damageprofiler/test/Length_plot_combined_data.svg
    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
    - path: output/damageprofiler/test/Length_plot.pdf
    - path: output/damageprofiler/test/lgdistribution.txt
      md5sum: df2e19195185ea9ee05e8e84b2948f36
    - path: output/damageprofiler/test/misincorporation.txt
      md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c

- name: damageprofiler_specieslist
  command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
  tags:
    - damageprofiler
  files:
    - path: output/damageprofiler/test/chr22/3p_freq_misincorporations.txt
      md5sum: de3b84d946a6b63cdcfadf82bf6854c0
    - path: output/damageprofiler/test/chr22/3pGtoA_freq.txt
      md5sum: 61c903b1504ed7d7182570dfc75e4498
    - path: output/damageprofiler/test/chr22/5pCtoT_freq.txt
      md5sum: 15a75b60ee519b61ce04a83fe3afe855
    - path: output/damageprofiler/test/chr22/5p_freq_misincorporations.txt
      md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
    - path: output/damageprofiler/test/chr22/DamagePlot_five_prime.svg
    - path: output/damageprofiler/test/chr22/DamagePlot.pdf
    - path: output/damageprofiler/test/chr22/DamagePlot_three_prime.svg
    - path: output/damageprofiler/test/DamageProfiler.log
      contains:
        - "FINISHED SUCCESSFULLY"
    - path: output/damageprofiler/test/chr22/dmgprof.json
      md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
    - path: output/damageprofiler/test/chr22/DNA_comp_genome.txt
      md5sum: fea48af1ecf491b439d36d4a919473df
    - path: output/damageprofiler/test/chr22/DNA_composition_sample.txt
      md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
    - path: output/damageprofiler/test/chr22/edit_distance.pdf
    - path: output/damageprofiler/test/chr22/edit_distance.svg
    - path: output/damageprofiler/test/chr22/editDistance.txt
      md5sum: 04d14b449a5afa8b5dbff0dfa762356b
    - path: output/damageprofiler/test/chr22/Length_plot_combined_data.svg
    - path: output/damageprofiler/test/chr22/Length_plot_forward_reverse_separated.svg
    - path: output/damageprofiler/test/chr22/Length_plot.pdf
    - path: output/damageprofiler/test/chr22/lgdistribution.txt
      md5sum: df2e19195185ea9ee05e8e84b2948f36
    - path: output/damageprofiler/test/chr22/misincorporation.txt
      md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c