name: snippy_core
description: Core-SNP alignment from Snippy outputs
keywords:
  - core
  - alignment
  - bacteria
tools:
  - snippy:
      description: "Rapid bacterial SNP calling and core genome alignments"
      homepage: "https://github.com/tseemann/snippy"
      documentation: "https://github.com/tseemann/snippy"
      tool_dev_url: "https://github.com/tseemann/snippy"
      doi: ""
      licence: "['GPL v2']"
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: Annotated variants in VCF format
      pattern: "*.vcf.gz"
  - aligned_fa:
      type: file
      description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)
      pattern: "*.aligned.fa.gz"
  - reference:
      type: file
      description: Reference genome in GenBank format
      pattern: "*.{gbk,gbk.gz,gbff,gbff.gz}"
  - mask:
      type: file
      description: Optional BED file of sites to mask
      pattern: "*.{bed}"
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"
  - aln:
      type: file
      description: A core SNP alignment in FASTA format
      pattern: "*.aln.gz"
  - full_aln:
      type: file
      description: A whole genome SNP alignment (includes invariant sites)
      pattern: "*.full.aln.gz"
  - clean_full_aln:
      type: file
      description: A whole genome SNP alignment (includes invariant sites) with Ns
      pattern: "*-clean.full.aln.gz"
  - tab:
      type: file
      description: Tab-separated columnar list of core SNP sites with alleles but NO annotations
      pattern: "*.tab"
  - vcf:
      type: file
      description: Multi-sample VCF file with genotype GT tags for all discovered alleles
      pattern: "*.vcf.gz"
  - txt:
      type: file
      description: Tab-separated columnar list of alignment/core-size statistics
      pattern: "*.txt"
authors:
  - "@rpetit3"
