- name: staphtyper-test
  command: bash -c 'nextflow run ./subworkflows/local/staphtyper/test.nf -entry test_staphtyper --wf staphtyper -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - staphtyper
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/staphtyper/merged-results/agrvate.tsv
      md5sum: b483a3d6ca1908ab813427b06751e51a
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/agrvate-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/agrvate-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/agrvate-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/agrvate-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/agrvate-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/agrvate-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/agrvate-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/agrvate-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/staphopiasccmec-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/staphopiasccmec-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/staphopiasccmec-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/staphopiasccmec-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/staphopiasccmec-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/staphopiasccmec-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/staphopiasccmec-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/logs/staphopiasccmec-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/staphtyper/merged-results/spatyper.tsv
      md5sum: 6afe7a90c591e32107d86c0e81029f54
    - path: bactopia/bactopia-runs/staphtyper/merged-results/staphopiasccmec.tsv
      md5sum: d02a33b227b96a95a99e18ca117a019d
    - path: bactopia/bactopia-runs/staphtyper/nf-reports/staphtyper-dag.dot
      contains: ['staphtyperdag', 'STAPHTYPER', 'versions']
    - path: bactopia/bactopia-runs/staphtyper/nf-reports/staphtyper-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/staphtyper/nf-reports/staphtyper-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/staphtyper/nf-reports/staphtyper-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000017085/tools/agrvate/GCF_000017085-agr_gp.tab
      md5sum: 04031d5b20fabcc4b3ddeef707e94029
    - path: bactopia/GCF_000017085/tools/agrvate/GCF_000017085-blastn_log.txt
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/agrvate/GCF_000017085-summary.tab
      md5sum: b483a3d6ca1908ab813427b06751e51a
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.err
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.log
      contains: ['agr', 'successful']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.out
      contains: ['agr', 'successful']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.sh
      contains: ['agrvate', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/versions.yml
      md5sum: 01aa0af82cd180a55f2bd342ef985100
    - path: bactopia/GCF_000017085/tools/spatyper/GCF_000017085.tsv
      md5sum: 6afe7a90c591e32107d86c0e81029f54
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.err
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.log
      contains: ['Spa', 'Repeats', 'spatyper']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.out
      contains: ['Spa', 'Repeats', 'spatyper']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.sh
      contains: ['spaTyper', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/versions.yml
      md5sum: 7fc367f432607840d76cdeea0d16e2f9
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/GCF_000017085.tsv
      md5sum: f631e5f4c80dc8ce004d72d9a3c56f58
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.err
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.log
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.out
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.sh
      contains: ['staphopia-sccmec', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/versions.yml
      md5sum: 75be8dadbe30d672a9dc6fbc360a3668
