name: quast
description: Quality Assessment Tool for Genome Assemblies
keywords:
  - quast
  - assembly
  - quality
  - contig
  - scaffold
tools:
  - quast:
      description: |
        QUAST calculates quality metrics for genome assemblies
      homepage: http://bioinf.spbau.ru/quast
      doi: 10.1093/bioinformatics/btt086
      licence: ["GPL-2.0-only"]
      identifier: biotools:quast
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - consensus:
        type: file
        description: |
          Fasta file containing the assembly of interest
        ontologies: []
  - - meta2:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: |
          The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.
        ontologies: []
  - - meta3:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - gff:
        type: file
        description: The genome GFF file. Has to contain at least a non-empty
          string dummy value.
        ontologies: []
output:
  results:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}:
          type: directory
          description: |
            Directory containing the results of the QUAST analysis
  tsv:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}.tsv:
          type: file
          description: TSV file
          pattern: "${prefix}.tsv"
          ontologies: []
  transcriptome:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}_transcriptome.tsv:
          type: file
          description: |
            Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided
          pattern: "${prefix}_transcriptome.tsv"
          ontologies: []
  misassemblies:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}_misassemblies.tsv:
          type: file
          description: |
            Report containing misassemblies, only when a reference fasta is provided
          pattern: "${prefix}_misassemblies.tsv"
          ontologies: []
  unaligned:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}_unaligned.tsv:
          type: file
          description: |
            Report containing unaligned contigs, only when a reference fasta is provided
          pattern: "${prefix}_unaligned.tsv"
          ontologies: []
  versions_quast:
    - - ${task.process}:
          type: string
          description: The name of the process
      - quast:
          type: string
          description: The name of the tool
      - quast.py --version 2>&1 | grep "QUAST" | sed 's/^.*QUAST v//; s/ .*\$//':
          type: eval
          description: The expression to obtain the version of the tool

topics:
  versions:
    - - ${task.process}:
          type: string
          description: The name of the process
      - quast:
          type: string
          description: The name of the tool
      - quast.py --version 2>&1 | grep "QUAST" | sed 's/^.*QUAST v//; s/ .*\$//':
          type: eval
          description: The expression to obtain the version of the tool

authors:
  - "@drpatelh"
  - "@kevinmenden"
maintainers:
  - "@drpatelh"
  - "@kevinmenden"
