- name: roary test_roary
  command: nextflow run ./tests/modules/roary -entry test_roary -c ./tests/config/nextflow.config -c ./tests/modules/roary/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: d4191cf748dd8016ad877857a034bef3
    - path: output/roary/results/accessory_binary_genes.fa.newick
      md5sum: d4a2a64e781263ca1b9b3a4bc9d3a6ea
    - 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="test1 test2 test3"']
    - 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
