- name: rgi-test
  command: bash -c 'nextflow run ./subworkflows/local/rgi/test.nf -entry test_rgi --wf rgi -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - rgi
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-concat/nf-merged-results.sh
      contains: ["csvtk", "END_VERSIONS"]
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/nf-merged-results.err
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/nf-merged-results.log
      contains: ['EPS', 'PNG', 'Rendering']
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/nf-merged-results.out
      contains: ['EPS', 'PNG', 'Rendering']
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/nf-merged-results.sh
      contains: ["rgi", "heatmap", "END_VERSIONS"]
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/versions.yml
      md5sum: c16a8469ca85a97204a631a52190323d
    - path: bactopia/bactopia-runs/rgi/merged-results/rgi-2.csv
      contains: ["gene", "Klebsiella", "Escherichia"]
    - path: bactopia/bactopia-runs/rgi/merged-results/rgi-2.eps
      contains: ["portrait", "end", "fill"]
    - path: bactopia/bactopia-runs/rgi/merged-results/rgi-2.png
    - path: bactopia/bactopia-runs/rgi/merged-results/rgi.tsv
      contains: ["ORF_ID", "disinfecting", "antibiotic"]
    - path: bactopia/bactopia-runs/rgi/nf-reports/rgi-dag.dot
      contains: ["rgidag", "RGI", "version"]
    - path: bactopia/bactopia-runs/rgi/nf-reports/rgi-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/rgi/nf-reports/rgi-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/rgi/nf-reports/rgi-trace.txt
      contains: ['task_id']
    - path: bactopia/GCA_000027305/tools/rgi/GCA_000027305.json
      contains: ["type_match", "model_name", "orf_dna_sequence"]
    - path: bactopia/GCA_000027305/tools/rgi/GCA_000027305.txt
      contains: ["ORF_ID", "disinfecting", "antibiotic"]
    - path: bactopia/GCA_000027305/tools/rgi/logs/nf-rgi.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCA_000027305/tools/rgi/logs/nf-rgi.err
    - path: bactopia/GCA_000027305/tools/rgi/logs/nf-rgi.log
    - path: bactopia/GCA_000027305/tools/rgi/logs/nf-rgi.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCA_000027305/tools/rgi/logs/nf-rgi.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCA_000027305/tools/rgi/logs/nf-rgi.sh
      contains: ["rgi", "main", "END_VERSIONS"]
    - path: bactopia/GCA_000027305/tools/rgi/logs/nf-rgi.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCA_000027305/tools/rgi/logs/versions.yml
      md5sum: 81482750f2ba727c718e24bf844293e8
    - path: bactopia/GCF_900478275/tools/rgi/GCF_900478275.json
      contains: ["type_match", "model_name", "orf_dna_sequence"]
    - path: bactopia/GCF_900478275/tools/rgi/GCF_900478275.txt
      contains: ["ORF_ID", "disinfecting", "antibiotic"]
    - path: bactopia/GCF_900478275/tools/rgi/logs/nf-rgi.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_900478275/tools/rgi/logs/nf-rgi.err
    - path: bactopia/GCF_900478275/tools/rgi/logs/nf-rgi.log
    - path: bactopia/GCF_900478275/tools/rgi/logs/nf-rgi.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_900478275/tools/rgi/logs/nf-rgi.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_900478275/tools/rgi/logs/nf-rgi.sh
      contains: ["rgi", "main", "END_VERSIONS"]
    - path: bactopia/GCF_900478275/tools/rgi/logs/nf-rgi.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_900478275/tools/rgi/logs/versions.yml
      md5sum: 81482750f2ba727c718e24bf844293e8
