nf-core_modules/modules/umitools/extract/meta.yml

name: umitools_extract
description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
keywords:
    - umitools
    - extract
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 ]
    - reads:
        type: list
        description: |
            List of input FASTQ files whose UMIs will be extracted.
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - reads:
        type: file
        description: Extracted FASTQ files. |
            For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
            For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
        pattern: "*.{fastq.gz}"
    - log:
        type: file
        description: Logfile for umi_tools
        pattern: "*.{log}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"

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