modules/umitools_extract

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

UMIbarcodeextractumitools

https://github.com/nf-core/modules/[...]/modules/nf-core/umitools/extract

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:map`

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

`reads:list`

List of input FASTQ files whose UMIs will be extracted.

Output

name:type

description

pattern

`reads`

`meta:map`

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

`*.fastq.gz: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`

`meta:map`

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

`*.log:file`

Logfile for umi_tools

*.{log}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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

modules/umitools_extract

Description

Input

`meta:map`

`reads:list`

Output

`reads`

`meta:map`

`*.fastq.gz:file`

`log`

`meta:map`

`*.log:file`

`versions`

`versions.yml:file`

Tools

umi_tools

included in

maintainers

get in touch