- name: mlst-test
  command: bash -c 'nextflow run ./subworkflows/local/mlst/test.nf -entry test_mlst --wf mlst -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - mlst
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/mlst/merged-results/logs/mlst-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/mlst/merged-results/logs/mlst-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/mlst/merged-results/logs/mlst-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/mlst/merged-results/logs/mlst-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/mlst/merged-results/logs/mlst-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/mlst/merged-results/logs/mlst-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/mlst/merged-results/logs/mlst-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/mlst/merged-results/logs/mlst-concat/versions.yml
      md5sum: 5909dd65afdda0a7f9db758c32aa0ae0
    - path: bactopia/bactopia-runs/mlst/merged-results/mlst.tsv
      md5sum: 67e1b29068b46c7ccd845ec36d41da89
    - path: bactopia/bactopia-runs/mlst/nf-reports/mlst-dag.dot
      contains: ['mlstdag', 'MLST', 'versions']
    - path: bactopia/bactopia-runs/mlst/nf-reports/mlst-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/mlst/nf-reports/mlst-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/mlst/nf-reports/mlst-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000017085/tools/mlst/GCF_000017085.tsv
      md5sum: 67e1b29068b46c7ccd845ec36d41da89
    - path: bactopia/GCF_000017085/tools/mlst/logs/nf-mlst.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/mlst/logs/nf-mlst.err
      contains: ['Found', 'Excluding', 'saureus', 'Done']
    - path: bactopia/GCF_000017085/tools/mlst/logs/nf-mlst.log
      contains: ['Found', 'Excluding', 'saureus', 'Done']
    - path: bactopia/GCF_000017085/tools/mlst/logs/nf-mlst.out
    - path: bactopia/GCF_000017085/tools/mlst/logs/nf-mlst.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/mlst/logs/nf-mlst.sh
      contains: ['mlst', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/mlst/logs/nf-mlst.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/mlst/logs/versions.yml
      md5sum: 6cdff5356823d7423f727b937f2685dd
