- name: mcroni-test
  command: bash -c 'nextflow run ./subworkflows/local/mcroni/test.nf -entry test_mcroni --wf mcroni -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - mcroni
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/mcroni/merged-results/logs/mcroni-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/mcroni/merged-results/logs/mcroni-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/mcroni/merged-results/logs/mcroni-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/mcroni/merged-results/logs/mcroni-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/mcroni/merged-results/logs/mcroni-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/mcroni/merged-results/logs/mcroni-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/mcroni/merged-results/logs/mcroni-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/mcroni/merged-results/logs/mcroni-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/mcroni/merged-results/mcroni.tsv
      contains: ['ISOLATE', 'GCF_001682305']
    - path: bactopia/bactopia-runs/mcroni/nf-reports/mcroni-dag.dot
      contains: ['mcronidag', 'MCRONI', 'versions']
    - path: bactopia/bactopia-runs/mcroni/nf-reports/mcroni-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/mcroni/nf-reports/mcroni-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/mcroni/nf-reports/mcroni-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_001682305/tools/mcroni/GCF_001682305_sequence.fa
      md5sum: 819b782ce2704d08e9cd4a43370e86c9
    - path: bactopia/GCF_001682305/tools/mcroni/GCF_001682305_table.tsv
      contains: ['ISOLATE', 'GCF_001682305']
    - path: bactopia/GCF_001682305/tools/mcroni/logs/nf-mcroni.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_001682305/tools/mcroni/logs/nf-mcroni.err
    - path: bactopia/GCF_001682305/tools/mcroni/logs/nf-mcroni.log
    - path: bactopia/GCF_001682305/tools/mcroni/logs/nf-mcroni.out
    - path: bactopia/GCF_001682305/tools/mcroni/logs/nf-mcroni.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_001682305/tools/mcroni/logs/nf-mcroni.sh
      contains: ['mcroni', 'END_VERSIONS']
    - path: bactopia/GCF_001682305/tools/mcroni/logs/nf-mcroni.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_001682305/tools/mcroni/logs/versions.yml
      md5sum: ec456fe8b15c9f3e55e0b4c0887c85e0
