nf-core/lofreq/call @ 0.0.0-3fc6d40
Summary
Lofreq subcommand to call low frequency variants from alignments
Get started
Add the following snippet to your workflow script to include this module.
include { LOFREQ_CALL } from 'nf-core/lofreq/call'
License
MIT License
Process
Name
|
LOFREQ_CALL |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM input file *.{bam}
|
intervals
file
|
BED file containing target regions for variant calling *.{bed}
|
fasta
file
|
The reference fasta file |
|---|
Output
2 channels
#1
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.vcf.gz
file
|
VCF output file *.{vcf}
|
#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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:19:28 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Flofreq%2Fcall/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/lofreq/call/blobs/sha256:92fcca349d8e8922ac2f618c5050f03da7c7261897bc789f7f1140c7f3076b2c |
| Size | 2.5 KB |
| Checksum | sha256:92fcca349d8e8922ac2f618c5050f03da7c7261897bc789f7f1140c7f3076b2c |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:27:54 (UTC) | 1 | 2.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:19:28 (UTC) | 1 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:14:19 (UTC) | 1 | 2.4 KB |