name: "pasty"
description: Serogroup Pseudomonas aeruginosa assemblies
keywords:
  - bacteria
  - serogroup
  - fasta
  - assembly
tools:
  - "pasty":
      description: "A tool for in silico serogrouping of Pseudomonas aeruginosa isolates"
      homepage: "https://github.com/rpetit3/pasty"
      documentation: "https://github.com/rpetit3/pasty"
      tool_dev_url: "https://github.com/rpetit3/pasty"
      doi: ""
      licence: "['Apache-2.0']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: An assembly in FASTA format
      pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - tsv:
      type: file
      description: A tab-delimited file with the predicted serogroup
      pattern: "*.tsv"
  - blast:
      type: file
      description: A tab-delimited file of all blast hits
      pattern: "*.blastn.tsv"
  - details:
      type: file
      description: A tab-delimited file with details for each serogroup
      pattern: "*.details.tsv"

authors:
  - "@rpetit3"