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
params:
  - outdir:
      type: string
      description: |
        The pipeline's output directory. By default, the module will
        output files into `$params.outdir/<SOFTWARE>`
  - publish_dir_mode:
      type: string
      description: |
        Value for the Nextflow `publishDir` mode parameter.
        Available: symlink, rellink, link, copy, copyNoFollow, move.
  - enable_conda:
      type: boolean
      description: |
        Run the module with Conda using the software specified
        via the `conda` directive
  - singularity_pull_docker_container:
      type: boolean
      description: |
        Instead of directly downloading Singularity images for use with Singularity,
        force the workflow to pull and convert Docker containers instead.

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

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

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