name: rsem_preparereference
description: Prepare a reference genome for RSEM
keywords:
  - rsem
  - reference
tools:
  - rseqc:
      description: |
        RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
      homepage: https://github.com/deweylab/RSEM
      documentation: https://github.com/deweylab/RSEM
      doi: https://doi.org/10.1186/1471-2105-12-323
input:
  - fasta:
      type: file
      description: The Fasta file of the reference genome
      pattern: "*.{fasta,fa}"
  - gtf:
      type: file
      description: The GTF file of the reference genome
      pattern: "*.gtf"
output:
  - rsem:
      type: directory
      description: RSEM index directory
      pattern: "rsem"
  - transcript_fasta:
      type: file
      description: Fasta file of transcripts
      pattern: "rsem/*transcripts.fa"
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
authors:
  - "@drpatelh"
  - "@kevinmenden"