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"