name: "snapaligner_single"
description: Performs single end fastq alignment to a fasta reference using SNAP
keywords:
  - alignment
  - map
  - fastq
  - bam
  - sam
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:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: List of single end input files
      pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
  - index:
      type: file
      description: List of SNAP genome index files
      pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"

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"
  - bam:
      type: file
      description: Aligned BAM file
      pattern: "*.{bam}"

authors:
  - "@matthdsm"