name: qualimap_bamqc description: Evaluate alignment data keywords: - quality control - qc - bam tools: - qualimap: description: | Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Interface and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. homepage: http://qualimap.bioinfo.cipf.es/ documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM file pattern: "*.{bam}" - gff: type: file description: Feature file with regions of interest pattern: "*.{gff,gtf,bed}" - use_gff: type: boolean description: Specifies if feature file should be used or not output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - results: type: dir description: Qualimap results dir pattern: "*/*" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@phue"