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"]
input:
  - consensus:
      type: file
      description: |
        Fasta file containing the assembly of interest
  - fasta:
      type: file
      description: |
        The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.
  - gff:
      type: file
      description: The genome GFF file. Has to contain at least a non-empty string dummy value.
output:
  - quast:
      type: directory
      description: Directory containing complete quast report
      pattern: "{prefix}/"
  - report:
      type: file
      description: tab-separated version of the summary, suitable for spreadsheets and mqc
      pattern: "${prefix}.tsv"
  - misassemblies:
      type: file
      description: |
        Report containing misassemblies, only when a reference fasta is provided
      pattern: "${prefix}_misassemblies.tsv"
  - transcriptome:
      type: file
      description: |
        Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided
      pattern: "${prefix}_transcriptome.tsv"
  - unaligned:
      type: file
      description: |
        Report containing unaligned contigs, only when a reference fasta is provided
      pattern: "${prefix}_unaligned.tsv"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@kevinmenden"
maintainers:
  - "@drpatelh"
  - "@kevinmenden"
