nf-core/umitools/extract @ 0.0.0-0c7146d
Summary
Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
Get started
Add the following snippet to your workflow script to include this module.
include { UMITOOLS_EXTRACT } from 'nf-core/umitools/extract'
License
MIT License
Process
Name
|
UMITOOLS_EXTRACT |
|---|
Input
1 channel
#1
tuple
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
3 channels
#1
log
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.log
file
|
Logfile for umi_tools *.{log}
|
#2
reads
tuple
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}
|
#3
versions_umitools
tuple
${task.process}
string
|
The name of the process |
|---|---|
umitools
string
|
The name of the tool |
umi_tools --version | sed -n '/version:/s/.*: //p'
eval
|
The expression to obtain the version of umitools |
| Tool | Description | Homepage |
|---|---|---|
| umi_tools | UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes | n/a |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:44:56 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fumitools%2Fextract/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/umitools/extract/blobs/sha256:60d88dae1a066cb0431bf90336c73aa2a7214af6bfd17abb94a07f71fbe8b676 |
| Size | 3.1 KB |
| Checksum | sha256:60d88dae1a066cb0431bf90336c73aa2a7214af6bfd17abb94a07f71fbe8b676 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:50:40 (UTC) | 3 | 3.1 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:44:56 (UTC) | 3 | 3.1 KB |