- name: gubbins-test
  command: bash -c 'nextflow run ./subworkflows/local/gubbins/test.nf -entry test_gubbins --wf gubbins -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - gubbins
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.branch_base_reconstruction.embl.gz
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.filtered_polymorphic_sites.fasta.gz
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.filtered_polymorphic_sites.phylip
      md5sum: 15efec56c27103e2f777d946a297d399
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.final_tree.tre
      md5sum: e1a69691e9ca439db36d1544f482f403
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.masked.aln.gz
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.node_labelled.final_tree.tre
      md5sum: accd0e5733897e53534c70dc24f8e74e
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.per_branch_statistics.csv
      md5sum: 2dc0dbae9a7cf545bfc56ac5d734342d
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.recombination_predictions.embl.gz
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.recombination_predictions.gff.gz
    - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.summary_of_snp_distribution.vcf.gz
    - path: bactopia/bactopia-runs/gubbins/gubbins/logs/gubbins.log
      contains: ["Process", "raxml", "Model", "Gubbins"]
    - path: bactopia/bactopia-runs/gubbins/gubbins/logs/nf-gubbins.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/gubbins/gubbins/logs/nf-gubbins.err
    - path: bactopia/bactopia-runs/gubbins/gubbins/logs/nf-gubbins.log
      contains: ["RAxML", "Alignment", "Substitution", "final"]
    - path: bactopia/bactopia-runs/gubbins/gubbins/logs/nf-gubbins.out
      contains: ["RAxML", "Alignment", "Substitution", "final"]
    - path: bactopia/bactopia-runs/gubbins/gubbins/logs/nf-gubbins.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/gubbins/gubbins/logs/nf-gubbins.sh
      contains: ["run_gubbins.py", "END_VERSIONS"]
    - path: bactopia/bactopia-runs/gubbins/gubbins/logs/nf-gubbins.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/gubbins/gubbins/logs/versions.yml
      md5sum: 0720185e5a55ffba81a6fd4828be73ee
    - path: bactopia/bactopia-runs/gubbins/nf-reports/gubbins-dag.dot
      contains: ['gubbinsdag', 'GUBBINS', 'versions']
    - path: bactopia/bactopia-runs/gubbins/nf-reports/gubbins-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/gubbins/nf-reports/gubbins-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/gubbins/nf-reports/gubbins-trace.txt
      contains: ['task_id']
