- name: gamma-test
  command: bash -c 'nextflow run ./subworkflows/local/gamma/test.nf -entry test_gamma --wf gamma -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - gamma
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/gamma/merged-results/gamma.tsv
      md5sum: b3995811a625996f8572cdf33b3f1c55
    - path: bactopia/bactopia-runs/gamma/merged-results/logs/gamma-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/gamma/merged-results/logs/gamma-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/gamma/merged-results/logs/gamma-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/gamma/merged-results/logs/gamma-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/gamma/merged-results/logs/gamma-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/gamma/merged-results/logs/gamma-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/gamma/merged-results/logs/gamma-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/gamma/merged-results/logs/gamma-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/gamma/nf-reports/gamma-dag.dot
      contains: ['gammadag', 'GAMMA', 'versions']
    - path: bactopia/bactopia-runs/gamma/nf-reports/gamma-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/gamma/nf-reports/gamma-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/gamma/nf-reports/gamma-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000292685/tools/gamma/gamma/GCF_000292685.gamma
      md5sum: b3995811a625996f8572cdf33b3f1c55
    - path: bactopia/GCF_000292685/tools/gamma/gamma/GCF_000292685.psl
      md5sum: aceb29eb63760fcbd5e48f973b47c391
    - path: bactopia/GCF_000292685/tools/gamma/gamma/logs/nf-gamma.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/gamma/gamma/logs/nf-gamma.err
    - path: bactopia/GCF_000292685/tools/gamma/gamma/logs/nf-gamma.log
      contains: ['Loaded', 'Searched', 'bases']
    - path: bactopia/GCF_000292685/tools/gamma/gamma/logs/nf-gamma.out
      contains: ['Loaded', 'Searched', 'bases']
    - path: bactopia/GCF_000292685/tools/gamma/gamma/logs/nf-gamma.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/gamma/gamma/logs/nf-gamma.sh
      contains: ['GAMMA', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/gamma/gamma/logs/nf-gamma.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/gamma/gamma/logs/versions.yml
      md5sum: 794590c9e7e331bfb9a2319c93892348
