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

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

It predicts variants using multiple processors

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @kaurravneet4123 @bjohnnyd

Maintainers: @kaurravneet4123 @bjohnnyd @nevinwu @AitorPeseta

It predicts variants using multiple processors

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

include { LOFREQ_CALLPARALLEL } from 'nf-core/lofreq/callparallel'

MIT License

Process

`Name`	`LOFREQ_CALLPARALLEL`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`bam` file	Tumor sample sorted BAM file `*.{bam}`
`bai` file	BAM index file `*.{bam.bai}`
`intervals` file	BED file containing target regions for variant calling `*.{bed}`

#2 tuple

`meta2` map	Groovy Map containing sample information about the reference fasta e.g. [ id:'reference' ]
`fasta` file	Reference genome FASTA file `*.{fasta}`

#3 tuple

`meta3` map	Groovy Map containing sample information about the reference fasta fai e.g. [ id:'reference' ]
`fai` file	Reference genome FASTA index file `*.{fai}`

Output 3 channels

#1 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz.tbi` file	Index of vcf file `*.{vcf.gz.tbi}`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	Predicted variants file `*.{vcf}`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
lofreq	Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors	https://csb5.github.io/lofreq/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:52:24 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Flofreq%2Fcallparallel/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/lofreq/callparallel/blobs/sha256:0fd9353614291dee8a01d977257f29eac6ac3aa16761c039f8e90b225bbe7eed
Size	2.9 KB
Checksum	sha256:0fd9353614291dee8a01d977257f29eac6ac3aa16761c039f8e90b225bbe7eed
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:52:24 (UTC)		1	2.9 KB	-