name: hisat2_align
description: Align RNA-Seq reads to a reference with HISAT2
keywords:
    - align
    - 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:
  - meta:
      type: map
      description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
          respectively.
  - index:
      type: file
      description: HISAT2 genome index file
      pattern: "*.ht2"
  - splicesites:
      type: file
      description: Splices sites in gtf file
      pattern: "*.{txt}"

output:
  - meta:
      type: map
      description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: Output BAM file containing read alignments
      pattern: "*.{bam}"
  - summary:
      type: file
      description: Aligment log
      pattern: "*.log"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@ntoda03"