name: salmon_quant
description: gene/transcript quantification with Salmon
keywords:
  - index
  - fasta
  - genome
  - reference
tools:
  - salmon:
      description: |
        Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
      homepage: https://salmon.readthedocs.io/en/latest/salmon.html
      manual: https://salmon.readthedocs.io/en/latest/salmon.html
      doi: 10.1038/nmeth.4197
      licence: ["GPL-3.0-or-later"]
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: directory
      description: Folder containing the star index files
  - gtf:
      type: file
      description: GTF of the reference transcriptome
  - transcriptome_fasta:
      type: file
      description: Fasta file of the reference transcriptome
  - alignment_mode:
    type: boolean
    description: whether to run salmon in alignment mode
  - lib_type:
    type: string
    description: |
      Override library type inferred based on strandedness defined in meta object

output:
  - sample_output:
      type: directory
      description: Folder containing the quantification results for a specific sample
      pattern: "${prefix}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@kevinmenden"
  - "@drpatelh"