nf-core/fgbio/fastqtobam @ 0.0.0-0c7146d
Summary
Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads
Get started
Add the following snippet to your workflow script to include this module.
include { FGBIO_FASTQTOBAM } from 'nf-core/fgbio/fastqtobam'
License
MIT License
Process
Name
|
FGBIO_FASTQTOBAM |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
reads
file
|
pair of reads to be converted into BAM file *.{fastq.gz}
|
Output
2 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.{bam,cram}
file
|
Unaligned, unsorted BAM or CRAM file *.{bam,cram}
|
#2
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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:39:15 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ffgbio%2Ffastqtobam/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/fgbio/fastqtobam/blobs/sha256:8caa3b803d0570e8159cd4597135b47ae5e92b84828a8e0286993903978506f5 |
| Size | 3.1 KB |
| Checksum | sha256:8caa3b803d0570e8159cd4597135b47ae5e92b84828a8e0286993903978506f5 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:39:15 (UTC) | 1 | 3.1 KB | - |