- name: ariba run test_ariba_run
  command: nextflow run ./tests/modules/ariba/run -entry test_ariba_run -c ./tests/config/nextflow.config  -c ./tests/modules/ariba/run/nextflow.config
  tags:
    - ariba
    - ariba/run
  files:
    - path: output/ariba/test/assembled_genes.fa.gz
    - path: output/ariba/test/assembled_seqs.fa.gz
    - path: output/ariba/test/assemblies.fa.gz
    - path: output/ariba/test/debug.report.tsv
      contains: ["ariba_ref_name", "reads", "free_text", "known_var_change"]
    - path: output/ariba/test/report.tsv
      contains: ["ariba_ref_name", "reads", "free_text", "known_var_change"]
    - path: output/ariba/test/version_info.txt
      contains: ["ARIBA", "Python", "OK", "True"]