- name: sistr-test
  command: bash -c 'nextflow run ./subworkflows/local/sistr/test.nf -entry test_sistr --wf sistr -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - sistr
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/sistr/merged-results/logs/sistr-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/sistr/merged-results/logs/sistr-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/sistr/merged-results/logs/sistr-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/sistr/merged-results/logs/sistr-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/sistr/merged-results/logs/sistr-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/sistr/merged-results/logs/sistr-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/sistr/merged-results/logs/sistr-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/sistr/merged-results/logs/sistr-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/sistr/merged-results/sistr.tsv
      contains: ['serogroup', 'Typhimurium', 'PASS']
    - path: bactopia/bactopia-runs/sistr/nf-reports/sistr-dag.dot
      contains: ['sistrdag', 'SISTR', 'version']
    - path: bactopia/bactopia-runs/sistr/nf-reports/sistr-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/sistr/nf-reports/sistr-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/sistr/nf-reports/sistr-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_016028495/tools/sistr/GCF_016028495-allele.fasta.gz
    - path: bactopia/GCF_016028495/tools/sistr/GCF_016028495-allele.json.gz
    - path: bactopia/GCF_016028495/tools/sistr/GCF_016028495-cgmlst.csv
      contains: ["NZ_AOXE01000052", "NC_003198"]
    - path: bactopia/GCF_016028495/tools/sistr/GCF_016028495.tsv
      contains: ['serogroup', 'Typhimurium', 'PASS']
    - path: bactopia/GCF_016028495/tools/sistr/logs/nf-sistr.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_016028495/tools/sistr/logs/nf-sistr.err
    - path: bactopia/GCF_016028495/tools/sistr/logs/nf-sistr.log
    - path: bactopia/GCF_016028495/tools/sistr/logs/nf-sistr.out
    - path: bactopia/GCF_016028495/tools/sistr/logs/nf-sistr.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_016028495/tools/sistr/logs/nf-sistr.sh
      contains: ['sistr', 'END_VERSIONS']
    - path: bactopia/GCF_016028495/tools/sistr/logs/nf-sistr.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_016028495/tools/sistr/logs/versions.yml
      md5sum: 9ce214ed7a2ba7b43b59e3a87553fccc
