---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "PhiSpy"
description: Predict prophages in bacterial genomes
keywords:
  - genomics
  - virus
  - phage
  - prophage
  - annotation
  - identification
tools:
  - "phispy":
      description: "Prophage finder using multiple metrics"
      homepage: "https://github.com/linsalrob/PhiSpy/blob/master/README.md"
      documentation: "https://github.com/linsalrob/PhiSpy/blob/master/README.md"
      tool_dev_url: "https://github.com/linsalrob/PhiSpy/"
      doi: "10.1093/nar/gks406"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

  - gbk:
      type: file
      description: Genome file in .gbk or .gbff format.
      pattern: "*.{gbk,gbff}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

  - coordinates:
      type: file
      description: |
        Coordinates of each prophage identified in the genome,
        and their att sites (if found).
      pattern: "*.{tsv}"

  - gbk:
      type: file
      description: |
        A duplicate GenBank record that is the same as the input record,
        but we have inserted the prophage information, including att
        sites into the record.
      pattern: "*.{gbk,gbff}"

  - log:
      type: file
      description: File containing the PhiSpy execution log
      pattern: "*.{log}"

  - information:
      type: file
      description: |
        File containing all the genes of the genome, one per line.
        The tenth column describes how likely the gene is a phage gene.
      pattern: "*.{tsv}"

  - bacteria_fasta:
      type: file
      description: Genome with prophage regions masked with N.
      pattern: "*.{fasta}"

  - bacteria_gbk:
      type: file
      description: Genome sequences identified as bacterial.
      pattern: "*.{gbk}"

  - phage_fasta:
      type: file
      description: Phage sequences extracted from the genome.
      pattern: "*.{fasta}"

  - phage_gbk:
      type: file
      description: Phage sequences extracted from the genome.
      pattern: "*.{gbk}"

  - prophage_gff:
      type: file
      description: Prophage information in GFF3 format.
      pattern: "*.{gff3}"

  - prophage_tbl:
      type: file
      description: |
        File containing prophage number and its location in the genome.
      pattern: "*.{tbl}"

  - prophage_tsv:
      type: file
      description: |
        A file containing simpler version of the coordinates file,
        with only prophage number, contig, start and stop.
      pattern: "*.{tsv}"

  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@jvfe"
