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"