nf-core/lofreq/somatic @ 0.0.0-0c7146d
Summary
Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
Get started
Add the following snippet to your workflow script to include this module.
include { LOFREQ_SOMATIC } from 'nf-core/lofreq/somatic'
License
MIT License
Process
Name
|
LOFREQ_SOMATIC |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
tumor
file
|
tumor sample input BAM file *.{bam}
|
tumor_index
file
|
tumor sample BAM index file *.{bam.bai}
|
normal
file
|
normal sample input BAM file *.{bam}
|
normal_index
file
|
normal sample BAM index file *.{bam.bai}
|
target_bed
file
|
BED file containing target regions for variant calling *.{bed}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information |
|---|---|
fasta
file
|
Reference genome FASTA file *.{fasta}
|
#3
tuple
meta3
map
|
Groovy Map containing reference information |
|---|---|
fai
file
|
Reference genome FASTA index file *.{fai}
|
Output
2 channels
#1
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.vcf.gz
file
|
Gzipped VCF file containing variants *.{vcf.gz}
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| lofreq | A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data | https://csb5.github.io/lofreq/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:52:30 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Flofreq%2Fsomatic/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/lofreq/somatic/blobs/sha256:daa7964d6a64692e78b9f619aa44a9b597633f8ddbaf46d1dd455befe00e0ab7 |
| Size | 2.9 KB |
| Checksum | sha256:daa7964d6a64692e78b9f619aa44a9b597633f8ddbaf46d1dd455befe00e0ab7 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:52:30 (UTC) | 1 | 2.9 KB | - |