- name: bactopia-prepare_help
  command: bash -c 'bin/bactopia/bactopia-prepare.py --help > bactopia-prepare.txt'
  tags:
    - bactopia
    - bactopia_help
    - bactopia_prepare
  files:
    - path: bactopia-prepare.txt
      contains: ['exit', 'bactopia', 'prepare', 'FASTQs']

- name: bactopia-prepare_example
  command: bash -c 'bin/bactopia/bactopia-prepare.py bactopia-tests/data/species/portiera/nanopore/ --ont > fastqs.txt'
  tags:
    - bactopia
    - bactopia_help
    - bactopia_prepare
  files:
    - path: fastqs.txt
      contains: ['sample', 'ERR3772599', 'ont', 'portiera']
