- name: roary test_roary
  command: nextflow run tests/modules/roary -entry test_roary -c tests/config/nextflow.config
  tags:
    - roary
  files:
    - path: output/roary/results/accessory.header.embl
      contains: ['ID   Genome standard; DNA; PRO; 1234 BP.']
    - path: output/roary/results/accessory.tab
      contains: ['FT']
    - path: output/roary/results/accessory_binary_genes.fa
      md5sum: 0baeea4947bf17a2bf29d43a44f0278f
    - path: output/roary/results/accessory_binary_genes.fa.newick
      md5sum: b1f8c76ab231bd38b850c1f8d3c1584b
    - path: output/roary/results/accessory_graph.dot
      contains: ['/* list of nodes */']
    - path: output/roary/results/blast_identity_frequency.Rtab
      md5sum: 829baa25c3fad94b1af207265452a692
    - path: output/roary/results/clustered_proteins
      contains: ['JKHLNHAL_00087']
    - path: output/roary/results/core_accessory.header.embl
      contains: ['ID   Genome standard; DNA; PRO; 1234 BP.']
    - path: output/roary/results/core_accessory.tab
      contains: ['FT                   /taxa="GCF_000292685 GCF_000298385 GCF_002849995"']
    - path: output/roary/results/core_accessory_graph.dot
      contains: ['/* list of nodes */']
    - path: output/roary/results/gene_presence_absence.Rtab
      contains: ['Gene']
    - path: output/roary/results/gene_presence_absence.csv
      contains: ['"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"']
    - path: output/roary/results/number_of_conserved_genes.Rtab
      contains: ['279']
    - path: output/roary/results/number_of_genes_in_pan_genome.Rtab
      contains: ['279']
    - path: output/roary/results/number_of_new_genes.Rtab
      contains: ['279']
    - path: output/roary/results/number_of_unique_genes.Rtab
      contains: ['279']
    - path: output/roary/results/summary_statistics.txt
      md5sum: 3921b5445df6a7ed59408119b8860a58