name: umi_tools
version: 1.0
description: Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. 
keywords:
    - UMI
    - RMT
    - Barcode
tools:
    - umi_tools:
        description: |
            Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. 
        homepage: https://github.com/CGATOxford/UMI-tools
        documentation: https://umi-tools.readthedocs.io/en/latest/
processes:
    - dedup:
        opperation: |
            Set command args to params.umitools_dedup_args
            The program will execute with the following pattern: umi_tools dedeup ARGS -I $bam -S SAMPLE_ID.dedup.bam --output-stats=SAMPLE_ID
        description: |
            Groups PCR duplicates and deduplicates reads to yield one read per group. 
            Use this when you want to remove the PCR duplicates prior to any downstream analysis.
        input:
            - sample_id:
                type: string
                description: Sample identifier
            - bai:
                type: file
                description: BAM file index
            - bam:
                type: file
                description: BAM sequence file
        output:
            - dedupBam:
                type: tuple
                description: A tuple of samples id and output bam file
                pattern: *SAMPLE_ID.dedup.bam
            - report:
                type: file
                description: Log file for the umi_tools opperation
                pattern: *SAMPLE_ID.dedup.log
authors:
    - @candiceh08
    - @chris-cheshire