name: "snapaligner_index"
description: Create a SNAP index for reference genome
keywords:
  - index
  - fasta
  - genome
  - reference
tools:
  - "snapaligner":
      description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
      homepage: "http://snap.cs.berkeley.edu"
      documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
      tool_dev_url: "https://github.com/amplab/snap"
      doi: "10.1101/2021.11.23.469039"
      licence: "['Apache v2']"
input:
  - fasta:
      type: file
      description: Input genome fasta file
  - altcontigfile:
      type: file
      description: Optional file with a list of alt contig names, one per line.
  - nonaltcontigfile:
      type: file
      description: Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.
  - altliftoverfile:
      type: file
      description: Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.
output:
  - index:
      type: file
      description: SNAP genome index files
      pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@matthdsm"