name: snpsites
description: Rapidly extracts SNPs from a multi-FASTA alignment.
keywords:
  - SNPs
  - invariant
  - constant
tools:
  - snpsites:
      description: Rapidly extracts SNPs from a multi-FASTA alignment.
      homepage: https://www.sanger.ac.uk/tool/snp-sites/
      documentation: https://github.com/sanger-pathogens/snp-sites
input:
  - alignment:
      type: file
      description: fasta alignment file
      pattern: "*.{fasta,fas,fa,aln}"
output:
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - fasta:
      type: file
      description: Variant fasta file
      pattern: "*.{fas}"
  - constant_sites:
      type: file
      description: Text file containing counts of constant sites
      pattern: "*.{sites.txt}"
authors:
  - "@avantonder"
