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:
        operation: |
            Set command args to params.umitools_dedup_args
            The program will execute with the following pattern:
                umi_tools dedup --log={SAMPLE_ID}.dedup.log {params.umitools_dedup_args} -I {SAMPLE_ID}.bam -S {SAMPLE_ID}.dedup.bam --output-stats={SAMPLE_ID}
        description: |
            Groups PCR duplicates and de-duplicates 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
            - bam:
                type: file array
                description: BAM sequence file and associated BAI index file
        output:
            - dedupBam:
                type: tuple
                description: A tuple of samples id and output bam file
                pattern: [sample_id, "*SAMPLE_ID.dedup.bam"]
            - dedupBam:
                type: tuple
                description: A tuple of samples id and output bai file
                pattern: [sample_id, "*SAMPLE_ID.dedup.bam.bai"]
            - report:
                type: file
                description: Log file for the umi_tools operation
                pattern: "*SAMPLE_ID.dedup.log"
authors:
    - "@candiceh08"
    - "@chris-cheshire"