---
name: "umicollapse"
description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
keywords:
  - umicollapse
  - deduplication
  - genomics
tools:
  - "umicollapse":
      description: "UMICollapse contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)."
      homepage: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse"
      documentation: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse"
      tool_dev_url: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse"
      doi: "10.7717/peerj.8275"
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: |
        BAM file containing reads to be deduplicated via UMIs.
      pattern: "*.{bam}"
  - bai:
      type: file
      description: |
        BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input.
      pattern: "*.{bai}"
  - mode:
      type: string
      description: |
        Selects the mode of Umicollapse - either fastq or bam need to be provided.
      pattern: "{fastq,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 deduplicated UMIs.
      pattern: "*.{bam}"
  - log:
      type: file
      description: A log file with the deduplication statistics.
      pattern: "*_{UMICollapse.log}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@CharlotteAnne"
  - "@chris-cheshire"
maintainers:
  - "@CharlotteAnne"
  - "@chris-cheshire"
  - "@apeltzer"
  - "@MatthiasZepper"
