- name: hicap-test
  command: bash -c 'nextflow run ./subworkflows/local/hicap/test.nf -entry test_hicap --wf hicap -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - hicap
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/hicap/merged-results/hicap.tsv
      contains: ['isolate', 'GCA_000027305', 'GCF_900478275']
    - path: bactopia/bactopia-runs/hicap/merged-results/logs/hicap-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/hicap/merged-results/logs/hicap-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/hicap/merged-results/logs/hicap-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/hicap/merged-results/logs/hicap-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/hicap/merged-results/logs/hicap-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/hicap/merged-results/logs/hicap-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/hicap/merged-results/logs/hicap-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/hicap/merged-results/logs/hicap-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/hicap/nf-reports/hicap-dag.dot
      contains: ['hicapdag', 'HICAP', 'versions']
    - path: bactopia/bactopia-runs/hicap/nf-reports/hicap-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/hicap/nf-reports/hicap-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/hicap/nf-reports/hicap-trace.txt
      contains: ['task_id']
    - path: bactopia/GCA_000027305/tools/hicap/GCA_000027305.tsv
      contains: ['isolate', 'GCA_000027305']
    - path: bactopia/GCA_000027305/tools/hicap/logs/nf-hicap.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCA_000027305/tools/hicap/logs/nf-hicap.err
      contains: ['dependencies', 'ORFs', 'Collecting']
    - path: bactopia/GCA_000027305/tools/hicap/logs/nf-hicap.log
      contains: ['dependencies', 'ORFs', 'Collecting']
    - path: bactopia/GCA_000027305/tools/hicap/logs/nf-hicap.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCA_000027305/tools/hicap/logs/nf-hicap.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCA_000027305/tools/hicap/logs/nf-hicap.sh
      contains: ['hicap', 'END_VERSIONS']
    - path: bactopia/GCA_000027305/tools/hicap/logs/nf-hicap.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCA_000027305/tools/hicap/logs/versions.yml
      md5sum: 406d486f223d7fb759cc7eeeda2bb4a8
    - path: bactopia/GCF_900478275/tools/hicap/GCF_900478275.gbk
      md5sum: 562d026956903354ac80721f501335d4
    - path: bactopia/GCF_900478275/tools/hicap/GCF_900478275.svg
      md5sum: 4fb94871dd0fdd8b4496049668176631
    - path: bactopia/GCF_900478275/tools/hicap/GCF_900478275.tsv
      contains: ['isolate', 'GCF_900478275']
    - path: bactopia/GCF_900478275/tools/hicap/logs/nf-hicap.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_900478275/tools/hicap/logs/nf-hicap.err
      contains: ['dependencies', 'ORFs', 'Collecting']
    - path: bactopia/GCF_900478275/tools/hicap/logs/nf-hicap.log
      contains: ['dependencies', 'ORFs', 'Collecting']
    - path: bactopia/GCF_900478275/tools/hicap/logs/nf-hicap.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_900478275/tools/hicap/logs/nf-hicap.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_900478275/tools/hicap/logs/nf-hicap.sh
      contains: ['hicap', 'END_VERSIONS']
    - path: bactopia/GCF_900478275/tools/hicap/logs/nf-hicap.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_900478275/tools/hicap/logs/versions.yml
      md5sum: 406d486f223d7fb759cc7eeeda2bb4a8
