- name: mobsuite-test
  command: bash -c 'nextflow run ./subworkflows/local/mobsuite/test.nf -entry test_mobsuite --wf mobsuite -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - mobsuite
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/mobsuite/merged-results/logs/mobsuite-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/mobsuite/merged-results/logs/mobsuite-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/mobsuite/merged-results/logs/mobsuite-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/mobsuite/merged-results/logs/mobsuite-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/mobsuite/merged-results/logs/mobsuite-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/mobsuite/merged-results/logs/mobsuite-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/mobsuite/merged-results/logs/mobsuite-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/mobsuite/merged-results/logs/mobsuite-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/mobsuite/merged-results/mobsuite.tsv
      md5sum: c76f770050665d308faa1a4720ab9ebe
    - path: bactopia/bactopia-runs/mobsuite/nf-reports/mobsuite-dag.dot
      contains: ['mobsuitedag', 'MOBSUITE', 'versions']
    - path: bactopia/bactopia-runs/mobsuite/nf-reports/mobsuite-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/mobsuite/nf-reports/mobsuite-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/mobsuite/nf-reports/mobsuite-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000017085/tools/mobsuite/GCF_000017085-mobtyper.txt
      md5sum: c76f770050665d308faa1a4720ab9ebe
    - path: bactopia/GCF_000017085/tools/mobsuite/chromosome.fasta
      md5sum: fe6e312b963fa5068c68cc25060ecd32
    - path: bactopia/GCF_000017085/tools/mobsuite/contig_report.txt
      contains: ["sample_id", "Staphylococcus", "plasmid"]
    - path: bactopia/GCF_000017085/tools/mobsuite/logs/nf-mobsuite.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/mobsuite/logs/nf-mobsuite.err
      contains: ["mob_suite", "Blasting", "MOB-recon"]
    - path: bactopia/GCF_000017085/tools/mobsuite/logs/nf-mobsuite.log
      contains: ["mob_suite", "Blasting", "MOB-recon"]
    - path: bactopia/GCF_000017085/tools/mobsuite/logs/nf-mobsuite.out
    - path: bactopia/GCF_000017085/tools/mobsuite/logs/nf-mobsuite.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/mobsuite/logs/nf-mobsuite.sh
      contains: ['mob_recon', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/mobsuite/logs/nf-mobsuite.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/mobsuite/logs/versions.yml
      md5sum: 70b7c16bd3f101f8ccf96a5640b7e2f8
    - path: bactopia/GCF_000017085/tools/mobsuite/plasmid_AA840.fasta
      md5sum: f774ed2069f1dfacd930673b748faaac
