name: dedup description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments). keywords: - dedup - deduplication - pcr duplicates - ancient DNA - paired-end - bam tools: - dedup: description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments). homepage: https://github.com/apeltzer/DeDup documentation: https://dedup.readthedocs.io/en/latest/ tool_dev_url: https://github.com/apeltzer/DeDup doi: "10.1186/s13059-016-0918-z" licence: ['GPL v3'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM/SAM file pattern: "*.{bam,sam}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - bam: type: file description: Deduplicated BAM file pattern: "*_rmdup.bam" - json: type: file description: JSON file for MultiQC pattern: "*.json" - hist: type: file description: Histogram data of amount of deduplication pattern: "*.hist" - log: type: file description: Dedup log information pattern: "*log" authors: - "@jfy133"