- name: mashtree-test
  command: bash -c 'nextflow run ./subworkflows/local/mashtree/test.nf -entry test_mashtree --wf mashtree -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - mashtree
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/mashtree/mashtree/logs/nf-mashtree.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/mashtree/mashtree/logs/nf-mashtree.err
      contains: ['mashtree', 'mashDistance', 'matrix']
    - path: bactopia/bactopia-runs/mashtree/mashtree/logs/nf-mashtree.log
      contains: ['mashtree', 'mashDistance', 'matrix']
    - path: bactopia/bactopia-runs/mashtree/mashtree/logs/nf-mashtree.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/mashtree/mashtree/logs/nf-mashtree.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/mashtree/mashtree/logs/nf-mashtree.sh
      contains: ['mashtree', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/mashtree/mashtree/logs/nf-mashtree.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/mashtree/mashtree/logs/versions.yml
      md5sum: 96538caf6e99cea2c6efe23f3b70bd9f
    - path: bactopia/bactopia-runs/mashtree/mashtree/mashtree.dnd
      contains: ['GCF_000009885', 'GCF_000017085']
    - path: bactopia/bactopia-runs/mashtree/mashtree/mashtree.tsv
      contains: ['GCF_000009885', 'GCF_000017085']
    - path: bactopia/bactopia-runs/mashtree/nf-reports/mashtree-dag.dot
      contains: ['mashtreedag', 'MASHTREE', 'versions']
    - path: bactopia/bactopia-runs/mashtree/nf-reports/mashtree-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/mashtree/nf-reports/mashtree-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/mashtree/nf-reports/mashtree-trace.txt
      contains: ['task_id']
