- name: gubbins
  command: nextflow run ./tests/software/gubbins -entry test_gubbins -c tests/config/nextflow.config
  tags:
    - gubbins
  files:
    - path: output/gubbins/test.filtered_polymorphic_sites.fasta
      md5sum: c9dff2294307eb2200a6e19efce47796
    - path: output/gubbins/test.recombination_predictions.embl
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/gubbins/test.recombination_predictions.gff
      md5sum: a2ca9c119674f4d121a8f78e4078fe05
    - path: output/gubbins/test.branch_base_reconstruction.embl
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/gubbins/test.summary_of_snp_distribution.vcf
      md5sum: afee50e92fb919a5df487fbda0b9dbb5
    - path: output/gubbins/test.per_branch_statistics.csv
      md5sum: 0f364b5e0b01a6be9b6a4407658ab25f
    - path: output/gubbins/test.filtered_polymorphic_sites.phylip
      md5sum: 85db9d0896cfec34a73641496b7498bb
    - path: output/gubbins/test.final_tree.tre
      md5sum: dce7164a0c69bb3d642a419907364aa3
    - path: output/gubbins/test.node_labelled.final_tree.tre
      md5sum: beef5ce05aca4598bb3f42caf126e045