Description

Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

reads{:bash}

:list

List of input FASTQ files whose UMIs will be extracted.

Output

name:type
description
pattern

reads{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.fastq.gz{:bash}

:file

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.

*.{fastq.gz}

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.log{:bash}

:file

Logfile for umi_tools

*.{log}

versions_umitools{:bash}

${task.process}{:bash}

:string

The name of the process

umitools{:bash}

:string

The name of the tool

umi_tools --version | sed -n '/version:/s/.*: //p'{:bash}

:eval

The expression to obtain the version of umitools

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

umitools{:bash}

:string

The name of the tool

umi_tools --version | sed -n '/version:/s/.*: //p'{:bash}

:eval

The expression to obtain the version of umitools

Tools

umi_tools

UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes

umi-tools.readthedocs.io/en/latest
included in
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maintainers
Github user drpatelh
Github user grst
get in touch
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