name: rseqc_junctionsaturation description: compare detected splice junctions to reference gene model keywords: - junctions - splicing - rnaseq tools: - rseqc: description: | RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: the alignment in bam format pattern: "*.{bam}" - bed: type: file description: a bed file for the reference gene model pattern: "*.{bed}" output: - pdf: type: file description: Junction saturation report pattern: "*.pdf" - rscript: type: file description: Junction saturation R-script pattern: "*.r" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden"