name: umitools_dedup
description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
keywords:
    - umitools
    - deduplication
tools:
    - umi_tools:
        description: >
            UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
            and single cell RNA-Seq cell barcodes
        documentation: https://umi-tools.readthedocs.io/en/latest/
        license: ['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.
        pattern: "*.{bai}"
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}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"

authors:
    - "@drpatelh"
    - "@grst"
    - "@klkeys"