- name: lissero-test
  command: bash -c 'nextflow run ./subworkflows/local/lissero/test.nf -entry test_lissero --wf lissero -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - all_tests
    - lissero
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/lissero/merged-results/lissero.tsv
      md5sum: f3fedfb8fe6789eaa389129d25c88d5f
    - path: bactopia/bactopia-runs/lissero/merged-results/logs/lissero-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/lissero/merged-results/logs/lissero-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/lissero/merged-results/logs/lissero-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/lissero/merged-results/logs/lissero-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/lissero/merged-results/logs/lissero-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/lissero/merged-results/logs/lissero-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/lissero/merged-results/logs/lissero-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/lissero/merged-results/logs/lissero-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/lissero/nf-reports/lissero-dag.dot
      contains: ['lisserodag', 'LISSERO', 'versions']
    - path: bactopia/bactopia-runs/lissero/nf-reports/lissero-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/lissero/nf-reports/lissero-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/lissero/nf-reports/lissero-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_002285835/tools/lissero/GCF_002285835.tsv
      md5sum: f3fedfb8fe6789eaa389129d25c88d5f
    - path: bactopia/GCF_002285835/tools/lissero/logs/nf-lissero.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_002285835/tools/lissero/logs/nf-lissero.err
      contains: ['lissero', 'Blastn']
    - path: bactopia/GCF_002285835/tools/lissero/logs/nf-lissero.log
      contains: ['lissero', 'Blastn']
    - path: bactopia/GCF_002285835/tools/lissero/logs/nf-lissero.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_002285835/tools/lissero/logs/nf-lissero.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_002285835/tools/lissero/logs/nf-lissero.sh
      contains: ['lissero', 'END_VERSIONS']
    - path: bactopia/GCF_002285835/tools/lissero/logs/nf-lissero.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_002285835/tools/lissero/logs/versions.yml
      md5sum: 822b9a47a51eb7c2b5e84d1c407a9150
