- name: gubbins
  command: nextflow run ./tests/modules/gubbins -entry test_gubbins -c tests/config/nextflow.config
  tags:
    - gubbins
  files:
    - path: output/gubbins/all_sites.filtered_polymorphic_sites.fasta
      md5sum: 4cbfd93868d8ed7d4d8b099eba137134
    - path: output/gubbins/all_sites.recombination_predictions.embl
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/gubbins/all_sites.recombination_predictions.gff
      md5sum: f95871e79968340cb82532e2c9b0c92b
    - path: output/gubbins/all_sites.branch_base_reconstruction.embl
      md5sum: 02e6fb268f7422bfe34b27ecd3b2c245
    - path: output/gubbins/all_sites.summary_of_snp_distribution.vcf
      md5sum: 276e62e888ea811577c8ffb2da0b3aff
    - path: output/gubbins/all_sites.per_branch_statistics.csv
      md5sum: 94b09b25d10504b56aa0307beae98a98
    - path: output/gubbins/all_sites.filtered_polymorphic_sites.phylip
      md5sum: 0a77f397a7797c5c3386832745b0c97a
    - path: output/gubbins/all_sites.final_tree.tre
      md5sum: e3c7ea18e2c5c49774c0e2ff78bd1818
    - path: output/gubbins/all_sites.node_labelled.final_tree.tre
      md5sum: 7727b4c4111ebf49cc8a4f1fdd25092c