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"