- name: amrfinderplus-test
  command: bash -c 'nextflow run ./subworkflows/local/amrfinderplus/test.nf -entry test_amrfinderplus --wf amrfinderplus -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - amrfinderplus
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/amrfinderplus-genes.tsv
      md5sum: a5cc7b0baa9e11c9a31540800d0a740c
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/amrfinderplus-proteins.tsv
      md5sum: f34365bb05512cb7bf1457184038a1f0
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-genes-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-genes-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-genes-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-genes-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-genes-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-genes-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-genes-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-genes-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-proteins-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-proteins-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-proteins-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-proteins-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-proteins-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-proteins-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-proteins-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/amrfinderplus/merged-results/logs/amrfinderplus-proteins-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/amrfinderplus/nf-reports/amrfinderplus-dag.dot
      contains: ['amrfinderplus', 'AMRFINDER', 'versions']
    - path: bactopia/bactopia-runs/amrfinderplus/nf-reports/amrfinderplus-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/amrfinderplus/nf-reports/amrfinderplus-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/amrfinderplus/nf-reports/amrfinderplus-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000292685/tools/amrfinderplus/GCF_000292685-genes.tsv
      md5sum: a5cc7b0baa9e11c9a31540800d0a740c
    - path: bactopia/GCF_000292685/tools/amrfinderplus/GCF_000292685-proteins.tsv
      md5sum: f34365bb05512cb7bf1457184038a1f0
    - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/nf-amrfinderplus.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/nf-amrfinderplus.err
      contains: ["amrfinder", "AMRFinder", "Running"]
    - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/nf-amrfinderplus.log
      contains: ["amrfinder", "AMRFinder", "Running"]
    - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/nf-amrfinderplus.out
      contains: ["Salmonella", "AMR_DNA", "Enterococcus_faecalis"]
    - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/nf-amrfinderplus.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/nf-amrfinderplus.sh
      contains: ['amrfinder', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/nf-amrfinderplus.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/versions.yml
      md5sum: 9933c8136bf5f0001ed5ec26405db0a7
