Nextflow Registry | nf-core/varlociraptor/preprocess@0.0.0-0c7146d

nf-core/varlociraptor/preprocess @ 0.0.0-0c7146d

Obtains per-sample observations for the actual calling process with varlociraptor calls

observations variants preprocessing

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @FriederikeHanssen

Maintainers: @FriederikeHanssen @famosab

Obtains per-sample observations for the actual calling process with varlociraptor calls

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

include { VARLOCIRAPTOR_PREPROCESS } from 'nf-core/varlociraptor/preprocess'

MIT License

Process

`Name`	`VARLOCIRAPTOR_PREPROCESS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	Sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`
`bai` file	Index of the BAM/CRAM/SAM file `*.{bai,crai,sai}`
`candidates` file	Sorted BCF/VCF file `*.{bcf,vcf,vcf.gz}`
`alignment_json` file	File containing alignment properties obtained with varlociraptor/estimatealignmentproperties `*.json`
`fasta` file	Reference fasta file `*.{fasta}`
`fai` file	Index for reference fasta file (must be with samtools index) `*.{fai}`

Output 2 channels

#1 bcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bcf` file	BCF file containing sample observations `*.bcf`

#2 versions_varlociraptor tuple

`${task.process}` string	The process the versions were collected from
`varlociraptor` string	The tool name
`varlociraptor --version \| sed 's/^varlociraptor //'` string	The command used to generate the version of the tool

Tool	Description	Homepage
varlociraptor	Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.	https://varlociraptor.github.io/docs/estimating/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:21:20 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvarlociraptor%2Fpreprocess/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/varlociraptor/preprocess/blobs/sha256:a1a774941430c7a6cdce85edc898f801d9d32d09f0e647ffaf6095250b44f208
Size	3.0 KB
Checksum	sha256:a1a774941430c7a6cdce85edc898f801d9d32d09f0e647ffaf6095250b44f208
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:21:20 (UTC)		1	3.0 KB	-