- name: pirate test_pirate
  command: nextflow run ./tests/modules/pirate -entry test_pirate -c ./tests/config/nextflow.config -c ./tests/modules/pirate/nextflow.config
  tags:
    - pirate
  files:
    - path: output/pirate/results/PIRATE.gene_families.ordered.tsv
      contains: ["allele_name"]
    - path: output/pirate/results/PIRATE.gene_families.tsv
      contains: ["allele_name"]
    - path: output/pirate/results/PIRATE.genomes_per_allele.tsv
      contains: ["g0197"]
    - path: output/pirate/results/PIRATE.log
      contains: ["PIRATE input options"]
    - path: output/pirate/results/PIRATE.pangenome_summary.txt
      md5sum: 4551c291bc06b21f984f25c09329ed7d
    - path: output/pirate/results/PIRATE.unique_alleles.tsv
      contains: ["allele_name"]
    - path: output/pirate/results/binary_presence_absence.fasta
      contains: ["GCF_000292685"]
    - path: output/pirate/results/binary_presence_absence.nwk
      md5sum: 5b5d86bf97d97de37bb9db514abb7762
    - path: output/pirate/results/cluster_alleles.tab
      contains: ["g0001"]
    - path: output/pirate/results/co-ords/GCF_000292685.co-ords.tab
      md5sum: d5ca0f06ca7ea1f5486683d5859bc9b8
    - path: output/pirate/results/co-ords/GCF_000298385.co-ords.tab
      md5sum: a24d6048b3074242bb558c7fa27a8b03
    - path: output/pirate/results/co-ords/GCF_002849995.co-ords.tab
      md5sum: 0c08228585f4fa95686e9b025e0fe9c1
    - path: output/pirate/results/genome2loci.tab
      md5sum: bbcea5bfcdcafe14a9aa7261c8e931b8
    - path: output/pirate/results/genome_list.txt
      md5sum: 6534b1635c258ad92b829077addc1ff5
    - path: output/pirate/results/link_clusters.log
      contains: ["parsing paralog file"]
    - path: output/pirate/results/loci_list.tab
      contains: ["GCF_000298385_00242"]
    - path: output/pirate/results/loci_paralog_categories.tab
      md5sum: 6404d2a32526a398f42d7da768a389bd
    - path: output/pirate/results/modified_gffs/GCF_000292685.gff
      md5sum: 2b73bda2f84dc634303dc90e641040ca
    - path: output/pirate/results/modified_gffs/GCF_000298385.gff
      md5sum: b1a9d6557d47e09249f08a7acdbbd618
    - path: output/pirate/results/modified_gffs/GCF_002849995.gff
      md5sum: 68532fc9bb639e6d83c731a069f60cf8
    - path: output/pirate/results/pan_sequences.fasta
      md5sum: ed835c77fdb20c36aa9d5208eb7ca0cb
    - path: output/pirate/results/pangenome.connected_blocks.tsv
      contains: ["block_number"]
    - path: output/pirate/results/pangenome.edges
      contains: ["g0259"]
    - path: output/pirate/results/pangenome.gfa
      contains: ["g0001"]
    - path: output/pirate/results/pangenome.order.tsv
      contains: ["g0172"]
    - path: output/pirate/results/pangenome.reversed.tsv
      md5sum: b2396ce09a6e4178761eca6dc7f4434f
    - path: output/pirate/results/pangenome.syntenic_blocks.tsv
      contains: ["g0091"]
    - path: output/pirate/results/pangenome.temp
    - path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
      contains: ["GCF_000298385_00242"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
      contains: ["GCF_000298385_00242"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
      contains: ["GCF_000298385_00242"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
      contains: ["GCF_000298385_00242"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
      contains: ["GCF_000298385_00242"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
      contains: ["GCF_000298385_00242"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
      contains: ["GCF_000298385_00242"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
      md5sum: 9da25d27684bfcc5488987ab2d1fd3a1
    - path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
      contains: ["GCF_000298385_00081"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
      contains: ["GCF_000298385_00242"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
      contains: ["chaos"]
    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
      md5sum: 84668b6c65b57026a17a50b0edd02541
    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pto
    - path: output/pirate/results/pangenome_log.txt
      contains: ["Creating pangenome on amino acid"]
    - path: output/pirate/results/paralog_clusters.tab
      contains: ["g0216"]
    - path: output/pirate/results/representative_sequences.faa
      contains: ["representative_genome"]
    - path: output/pirate/results/representative_sequences.ffn
      contains: ["representative_genome"]
    - path: output/pirate/results/split_groups.log
      contains: ["g0213"]