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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:20:46 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fumitools%2Fextract/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/umitools/extract/blobs/sha256:1f5ba9bf9ce74975c4ddce5a6bb68c73c4e7372770854575dce08464329e4e6d |
| Size | 3.1 KB |
| Checksum | sha256:1f5ba9bf9ce74975c4ddce5a6bb68c73c4e7372770854575dce08464329e4e6d |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:20:46 (UTC) | 1 | 3.1 KB | - |