- name: roary-test
  command: bash -c 'nextflow run ./subworkflows/local/roary/test.nf -entry test_roary --wf roary -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - roary
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/roary/nf-reports/roary-dag.dot
      contains: ['roarydag', 'ROARY', 'versions']
    - path: bactopia/bactopia-runs/roary/nf-reports/roary-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/roary/nf-reports/roary-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/roary/nf-reports/roary-trace.txt
      contains: ['task_id']
    - path: bactopia/bactopia-runs/roary/roary/accessory.header.embl
      contains: ['ID   Genome standard; DNA; PRO; 1234 BP.']
    - path: bactopia/bactopia-runs/roary/roary/accessory.tab
      contains: ['FT']
    - path: bactopia/bactopia-runs/roary/roary/accessory_binary_genes.fa.gz
    - path: bactopia/bactopia-runs/roary/roary/accessory_binary_genes.fa.newick
      md5sum: b1f8c76ab231bd38b850c1f8d3c1584b
    - path: bactopia/bactopia-runs/roary/roary/accessory_graph.dot
      contains: ['/* list of nodes */']
    - path: bactopia/bactopia-runs/roary/roary/blast_identity_frequency.Rtab
      md5sum: 829baa25c3fad94b1af207265452a692
    - path: bactopia/bactopia-runs/roary/roary/clustered_proteins
      contains: ['JKHLNHAL_00087']
    - path: bactopia/bactopia-runs/roary/roary/core-genome.aln.gz
    - path: bactopia/bactopia-runs/roary/roary/core_accessory.header.embl
      contains: ['ID   Genome standard; DNA; PRO; 1234 BP.']
    - path: bactopia/bactopia-runs/roary/roary/core_accessory.tab
      contains: ['FT                   /taxa="GCF_000292685 GCF_000298385 GCF_002849995"']
    - path: bactopia/bactopia-runs/roary/roary/core_accessory_graph.dot
      contains: ['/* list of nodes */']
    - path: bactopia/bactopia-runs/roary/roary/core_alignment_header.embl
      contains: ['ID   Genome standard; DNA; PRO; 1234 BP.']
    - path: bactopia/bactopia-runs/roary/roary/core_gene_alignment.aln.gz
    - path: bactopia/bactopia-runs/roary/roary/gene_presence_absence.Rtab
      contains: ['Gene']
    - path: bactopia/bactopia-runs/roary/roary/gene_presence_absence.csv
      contains: ['"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"']
    - path: bactopia/bactopia-runs/roary/roary/logs/nf-roary.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/roary/roary/logs/nf-roary.err
    - path: bactopia/bactopia-runs/roary/roary/logs/nf-roary.log
      contains: ['cite', 'Roary']
    - path: bactopia/bactopia-runs/roary/roary/logs/nf-roary.out
    - path: bactopia/bactopia-runs/roary/roary/logs/nf-roary.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/roary/roary/logs/nf-roary.sh
      contains: ['roary', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/roary/roary/logs/nf-roary.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/roary/roary/logs/versions.yml
      md5sum: 3b710eef62b3be64755079699ae4aae1
    - path: bactopia/bactopia-runs/roary/roary/number_of_conserved_genes.Rtab
      contains: ['2']
    - path: bactopia/bactopia-runs/roary/roary/number_of_genes_in_pan_genome.Rtab
      contains: ['2']
    - path: bactopia/bactopia-runs/roary/roary/number_of_new_genes.Rtab
      contains: ['2']
    - path: bactopia/bactopia-runs/roary/roary/number_of_unique_genes.Rtab
      contains: ['2']
    - path: bactopia/bactopia-runs/roary/roary/pan_genome_reference.fa.gz
    - path: bactopia/bactopia-runs/roary/roary/summary_statistics.txt
      md5sum: 3921b5445df6a7ed59408119b8860a58
