nf-core/fgbio/groupreadsbyumi @ 0.0.0-0c7146d
Summary
Groups reads together that appear to have come from the same original molecule. Reads are grouped by template, and then templates are sorted by the 5’ mapping positions of the reads from the template, used from earliest mapping position to latest. Reads that have the same end positions are then sub-grouped by UMI sequence. (!) Note: the MQ tag is required on reads with mapped mates (!) This can be added using samblaster with the optional argument --addMateTags.
Get started
Add the following snippet to your workflow script to include this module.
include { FGBIO_GROUPREADSBYUMI } from 'nf-core/fgbio/groupreadsbyumi'
License
MIT License
Name
|
FGBIO_GROUPREADSBYUMI |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM file. Note: the MQ tag is required on reads with mapped mates (!) *.bam
|
strategy
string
|
Required argument: defines the UMI assignment strategy. Must be chosen among: Identity, Edit, Adjacency, Paired. |
|---|
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
UMI-grouped BAM *.bam
|
histogram
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*histogram.txt
file
|
A text file containing the tag family size counts *.txt
|
read_metrics
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*read-metrics.txt
file
|
A text file containing the read count metrics from grouping *.txt
|
versions_fgbio
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
fgbio
string
|
The tool name |
fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| fgbio | A set of tools for working with genomic and high throughput sequencing data, including UMIs | http://fulcrumgenomics.github.io/fgbio/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:01:02 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Ffgbio%2Fgroupreadsbyumi/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/fgbio/groupreadsbyumi/blobs/sha256:77d2fec19c0358cf8f04b787b2db99989c21682595baf6ee93d5224a9534b561 |
| Size | 3.2 KB |
| Checksum | sha256:77d2fec19c0358cf8f04b787b2db99989c21682595baf6ee93d5224a9534b561 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:17:18 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:01:02 (UTC) | 3 | 3.2 KB |