name: "universc"
description: Module to run UniverSC an open-source pipeline to demultiplex and process single-cell RNA-Seq data
keywords:
  - demultiplex
  - align
  - single-cell
  - scRNA-Seq
  - count
  - umi
tools:
  - "universc":
      description: "UniverSC: a flexible cross-platform single-cell data processing pipeline"
      homepage: "https://hub.docker.com/r/tomkellygenetics/universc"
      documentation: "https://raw.githubusercontent.com/minoda-lab/universc/master/man/launch_universc.sh"
      tool_dev_url: "https://github.com/minoda-lab/universc"
      doi: "10.1101/2021.01.19.427209"
      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: FASTQ or FASTQ.GZ file, list of 2 files for paired-end data
      pattern: "*.{fastq,fq,fastq.gz,fq.gz}"

output:
  - outs:
      type: file
      description: Files containing the outputs of Cell Ranger
      pattern: "sample-${meta.id}/outs/*"
  - versions:
      type: file
      description: File containing software version
      pattern: "versions.yml"

authors:
  - "@kbattenb"
  - "@tomkellygenetics"
