name: hisat2_build
description: Builds HISAT2 index for reference genome
keywords:
  - build
  - index
  - fasta
  - genome
  - reference
tools:
  - hisat2:
      description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
      homepage: https://daehwankimlab.github.io/hisat2/
      documentation: https://daehwankimlab.github.io/hisat2/manual/
      doi: "10.1038/s41587-019-0201-4"
      licence: ["MIT"]

input:
  - fasta:
      type: file
      description: Reference fasta file
      pattern: "*.{fa,fasta,fna}"
  - gtf:
      type: file
      description: Reference gtf annotation file
      pattern: "*.{gtf}"
  - splicesites:
      type: file
      description: Splices sites in gtf file
      pattern: "*.{txt}"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - index:
      type: file
      description: HISAT2 genome index file
      pattern: "*.ht2"

authors:
  - "@ntoda03"