- name: pirate-test
  command: bash -c 'nextflow run ./subworkflows/local/pirate/test.nf -entry test_pirate --wf pirate -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - pirate
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/pirate/nf-reports/pirate-dag.dot
      contains: ['piratedag', 'PIRATE', 'versions']
    - path: bactopia/bactopia-runs/pirate/nf-reports/pirate-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/pirate/nf-reports/pirate-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/pirate/nf-reports/pirate-trace.txt
      contains: ['task_id']
    - path: bactopia/bactopia-runs/pirate/pirate/PIRATE.gene_families.ordered.tsv
      contains: ['allele_name']
    - path: bactopia/bactopia-runs/pirate/pirate/PIRATE.gene_families.tsv
      contains: ['allele_name']
    - path: bactopia/bactopia-runs/pirate/pirate/PIRATE.genomes_per_allele.tsv
      contains: ['g0197']
    - path: bactopia/bactopia-runs/pirate/pirate/PIRATE.pangenome_summary.txt
      md5sum: 645e3b52d4bb3539926205cd7d80a7fd
    - path: bactopia/bactopia-runs/pirate/pirate/PIRATE.unique_alleles.tsv
      contains: ['allele_name']
    - path: bactopia/bactopia-runs/pirate/pirate/binary_presence_absence.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/binary_presence_absence.nwk
      md5sum: 778695ee4fa2b02241731cc44ce927fb
    - path: bactopia/bactopia-runs/pirate/pirate/cluster_alleles.tab
      contains: ['g0001']
    - path: bactopia/bactopia-runs/pirate/pirate/co-ords/GCF_000292685.co-ords.tab
      md5sum: d5ca0f06ca7ea1f5486683d5859bc9b8
    - path: bactopia/bactopia-runs/pirate/pirate/co-ords/GCF_000298385.co-ords.tab
      md5sum: a24d6048b3074242bb558c7fa27a8b03
    - path: bactopia/bactopia-runs/pirate/pirate/co-ords/GCF_000300075.co-ords.tab
      md5sum: 21532b58b708a0ea2490f7e9509982e7
    - path: bactopia/bactopia-runs/pirate/pirate/co-ords/GCF_002849995.co-ords.tab
      md5sum: 0c08228585f4fa95686e9b025e0fe9c1
    - path: bactopia/bactopia-runs/pirate/pirate/co-ords/GCF_902713755.co-ords.tab
      md5sum: 6bea5163af8f9612821166c3a069dd56
    - path: bactopia/bactopia-runs/pirate/pirate/core-genome.aln.gz
    - path: bactopia/bactopia-runs/pirate/pirate/core_alignment.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/core_alignment.gff
      contains: ['Pangenome', 'CDS', 'tRNA']
    - path: bactopia/bactopia-runs/pirate/pirate/feature_sequences/g0001.aa.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/feature_sequences/g0001.nucleotide.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/feature_sequences/g0002.aa.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/feature_sequences/g0002.nucleotide.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/feature_sequences/g0284.aa.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/feature_sequences/g0284.nucleotide.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/feature_sequences/g0285.aa.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/feature_sequences/g0285.nucleotide.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/gene_presence_absence.csv
      contains: ['GCF_000', 'hypothetical', 'Gene']
    - path: bactopia/bactopia-runs/pirate/pirate/genome2loci.tab
      contains: ['GCF_000', 'hypothetical']
    - path: bactopia/bactopia-runs/pirate/pirate/genome_list.txt
      contains: ['GCF_002849995', 'GCF_000292685']
    - path: bactopia/bactopia-runs/pirate/pirate/loci_list.tab
      contains: ['GCF_000298385_00242']
    - path: bactopia/bactopia-runs/pirate/pirate/loci_paralog_categories.tab
      contains: ['GCF_000', 'g0']
    - path: bactopia/bactopia-runs/pirate/pirate/logs/nf-pirate.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/pirate/pirate/logs/nf-pirate.err
    - path: bactopia/bactopia-runs/pirate/pirate/logs/nf-pirate.log
      contains: ['PIRATE', 'completed']
    - path: bactopia/bactopia-runs/pirate/pirate/logs/nf-pirate.out
      contains: ['PIRATE', 'completed']
    - path: bactopia/bactopia-runs/pirate/pirate/logs/nf-pirate.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/pirate/pirate/logs/nf-pirate.sh
      contains: ['pirate', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/pirate/pirate/logs/nf-pirate.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/pirate/pirate/logs/results/PIRATE.log
      contains: ['PIRATE input options']
    - path: bactopia/bactopia-runs/pirate/pirate/logs/results/link_clusters.log
      contains: ['parsing paralog file']
    - path: bactopia/bactopia-runs/pirate/pirate/logs/results/split_groups.log
      contains: ['g0']
    - path: bactopia/bactopia-runs/pirate/pirate/logs/versions.yml
      md5sum: fbda8822b425f63332e8d3d64ae6c787
    - path: bactopia/bactopia-runs/pirate/pirate/modified_gffs/GCF_000292685.gff
      md5sum: 2b73bda2f84dc634303dc90e641040ca
    - path: bactopia/bactopia-runs/pirate/pirate/modified_gffs/GCF_000298385.gff
      md5sum: b1a9d6557d47e09249f08a7acdbbd618
    - path: bactopia/bactopia-runs/pirate/pirate/modified_gffs/GCF_000300075.gff
      md5sum: 082185a0e46efe63d60d1ff5311c80bc
    - path: bactopia/bactopia-runs/pirate/pirate/modified_gffs/GCF_002849995.gff
      md5sum: 68532fc9bb639e6d83c731a069f60cf8
    - path: bactopia/bactopia-runs/pirate/pirate/modified_gffs/GCF_902713755.gff
      md5sum: c9b95a4c325c8df4c7430137b0adacbd
    - path: bactopia/bactopia-runs/pirate/pirate/pan_sequences.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome.connected_blocks.tsv
      contains: ['block_number']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome.edges
      contains: ['g0259']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome.gfa
      contains: ['g0001']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome.order.tsv
      contains: ['g0172']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome.reversed.tsv
      md5sum: b2396ce09a6e4178761eca6dc7f4434f
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome.syntenic_blocks.tsv
      contains: ['g0091']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome.temp
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_alignment.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_alignment.gff
      contains: ['Pangenome', 'CDS', 'tRNA']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.50.reclustered.reinflated
      contains: ['GCF_000298385_00242']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.60.reclustered.reinflated
      contains: ['GCF_000298385_00242']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.70.reclustered.reinflated
      contains: ['GCF_000298385_00242']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.80.reclustered.reinflated
      contains: ['GCF_000298385_00242']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.90.reclustered.reinflated
      contains: ['GCF_000298385_00242']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.95.reclustered.reinflated
      contains: ['GCF_000298385_00242']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.98.reclustered.reinflated
      contains: ['GCF_000298385_00242']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.blast.output
      contains: ['GCF_002849995', 'GCF_000292685']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.cdhit_clusters
      contains: ['GCF_000298385_00081']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.core_clusters.tab
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.mcl_log.txt
      contains: ['chaos']
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.representative.fasta.gz
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.representative.fasta.pdb
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.representative.fasta.pot
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.representative.fasta.ptf
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_iterations/pan_sequences.representative.fasta.pto
    - path: bactopia/bactopia-runs/pirate/pirate/pangenome_log.txt
      contains: ['Creating pangenome on amino acid']
    - path: bactopia/bactopia-runs/pirate/pirate/paralog_clusters.tab
      contains: ['g0']
    - path: bactopia/bactopia-runs/pirate/pirate/representative_sequences.faa
      contains: ['representative_genome']
    - path: bactopia/bactopia-runs/pirate/pirate/representative_sequences.ffn
      contains: ['representative_genome']
