- name: ariba-test
  command: bash -c 'nextflow run ./subworkflows/local/ariba/test.nf -entry test_ariba --wf ariba --ariba_dir ariba --ariba_db card -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - ariba
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/ariba/merged-results/card-report.tsv
      contains: ["ariba_ref_name", "reads", "resistance", "Clostridioides"]
    - path: bactopia/bactopia-runs/ariba/merged-results/card-summary.csv
      contains: ["name", "novel_var", "Clostridioides"]
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.begin
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.err
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.log
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.out
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.sh
      contains: ['csvtk', 'concat', "END_VERSIONS"]
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/versions.yml
      md5sum: 344624d16fe24cfad6e9f45a19be708f
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.begin
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.err
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.log
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.out
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.sh
      contains: ['csvtk', 'concat', "END_VERSIONS"]
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/versions.yml
      md5sum: 6551889c4545016b96a75751d9efdb38
    - path: bactopia/bactopia-runs/ariba/nf-reports/ariba-dag.dot
      contains: ['aribadag', 'ARIBA', 'versions']
    - path: bactopia/bactopia-runs/ariba/nf-reports/ariba-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/ariba/nf-reports/ariba-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/ariba/nf-reports/ariba-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/ariba/card/SRR2838702-report.tsv
      contains: ["ariba_ref_name", "reads", "resistance", "Clostridioides"]
    - path: bactopia/SRR2838702/tools/ariba/card/SRR2838702-summary.csv
      contains: ["name", "novel_var", "Clostridioides"]
    - path: bactopia/SRR2838702/tools/ariba/card/assembled_genes.fa.gz
    - path: bactopia/SRR2838702/tools/ariba/card/assembled_seqs.fa.gz
    - path: bactopia/SRR2838702/tools/ariba/card/assemblies.fa.gz
    - path: bactopia/SRR2838702/tools/ariba/card/debug.report.tsv
      contains: ["ariba_ref_name", "reads", "resistance"]
    - path: bactopia/SRR2838702/tools/ariba/card/log.clusters.gz
    - path: bactopia/SRR2838702/tools/ariba/card/logs/nf-ariba.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ariba/card/logs/nf-ariba.err
      contains: ["filtering"]
    - path: bactopia/SRR2838702/tools/ariba/card/logs/nf-ariba.log
      contains: ["card", "Making", "done!", "filtering"]
    - path: bactopia/SRR2838702/tools/ariba/card/logs/nf-ariba.out
      contains: ["card", "Making", "done!"]
    - path: bactopia/SRR2838702/tools/ariba/card/logs/nf-ariba.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/ariba/card/logs/nf-ariba.sh
      contains: ['ariba', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/ariba/card/logs/nf-ariba.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/ariba/card/logs/versions.yml
      md5sum: 033ed5d08925ede510a221561b454bbc
    - path: bactopia/SRR2838702/tools/ariba/card/version_info.txt
      contains: ["ARIBA", "Python", "OK", "True"]
