name: rsem_calculateexpression description: Calculate expression with RSEM keywords: - rsem - expression - quantification 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: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: Input reads for quantification pattern: "*.fastq.gz"# - index: type: file description: RSEM index pattern: "rsem/*" output: - counts_gene: type: file description: Expression counts on gene level pattern: "*.genes.results" - counts_transctips: type: file description: Expression counts on transcript level pattern: "*.isoforms.results" - stat: type: file description: RSEM statistics pattern: "*.stat" - logs: type: file description: RSEM logs pattern: "*.log" - version: type: file description: File containing software version pattern: "*.{version.txt}" - bam_star: type: file description: BAM file generated by STAR (optional) pattern: "*.STAR.genome.bam" - bam_genome: type: file description: Genome BAM file (optional) pattern: "*.genome.bam" - bam_transcript: type: file description: Transcript BAM file (optional) pattern: "*.transcript.bam" authors: - "@drpatelh" - "@kevinmenden"