name: picard_markduplicates description: Locate and tag duplicate reads in a BAM file keywords: - markduplicates - pcr - duplicates - bam - sam - cram tools: - picard: description: | A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ 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}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM file with duplicate reads marked/removed pattern: "*.{bam}" - bai: type: file description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag pattern: "*.{bai}" - metrics: type: file description: Duplicate metrics file generated by picard pattern: "*.{metrics.txt}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@drpatelh" - "@projectoriented"