nf-core/lofreq/viterbi @ 0.0.0-3fc6d40
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_VITERBI } from 'nf-core/lofreq/viterbi'
License
MIT License
Process
Name
|
LOFREQ_VITERBI |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
bam
file
|
Sorted BAM file *.{bam}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information about the reference fasta e.g. [ id:'reference' ] |
|---|---|
fasta
file
|
Reference genome FASTA file *.{fasta}
|
Output
2 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.bam
file
|
Realignment and sorted BAM file *.{bam}
|
#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 15:19:35 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Flofreq%2Fviterbi/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/lofreq/viterbi/blobs/sha256:f882cd57522dfb92d0988ba584beb8cce1f2de24946a2eb1ab7fd6f744a9dce8 |
| Size | 2.4 KB |
| Checksum | sha256:f882cd57522dfb92d0988ba584beb8cce1f2de24946a2eb1ab7fd6f744a9dce8 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:28:00 (UTC) | 3 | 2.4 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:19:35 (UTC) | 4 | 2.4 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:14:29 (UTC) | 4 | 2.4 KB |