Nextflow Registry | nf-core/lofreq/call@0.0.0-0c7146d

nf-core/lofreq/call @ 0.0.0-0c7146d

Lofreq subcommand to call low frequency variants from alignments

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @bjohnnyd

Maintainers: @bjohnnyd

Lofreq subcommand to call low frequency variants from alignments

Add the following snippet to your workflow script to include this module.

include { LOFREQ_CALL } from 'nf-core/lofreq/call'

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:52:23 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Flofreq%2Fcall/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/lofreq/call/blobs/sha256:2033474e4586e4bcd458ca7406cd188ef8e33ded91412cc6b104ebb317a8e71b
Size	2.5 KB
Checksum	sha256:2033474e4586e4bcd458ca7406cd188ef8e33ded91412cc6b104ebb317a8e71b
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:52:23 (UTC)		1	2.5 KB	-