Nextflow Registry | nf-core/paragraph/multigrmpy@0.0.0-0c7146d

nf-core/paragraph/multigrmpy @ 0.0.0-0c7146d

Genotype structural variants using paragraph and grmpy

vcf json structural variants graphs genotyping

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Genotype structural variants using paragraph and grmpy

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

include { PARAGRAPH_MULTIGRMPY } from 'nf-core/paragraph/multigrmpy'

MIT License

Process

`Name`	`PARAGRAPH_MULTIGRMPY`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`variants` file	A VCF or JSON file containing called structural variants `*.{vcf,json}`
`variants_index` file	The index for the VCF file `*.tbi`
`reads` file	BAM or CRAM file(s) to genotype against. These should be specified inside the `manifest` `*.{bam,cram}`
`reads_index` file	The index/indices for the BAM/CRAM file(s) `*.{bai,crai}`
`manifest` file	A tab separated file containing information on the BAM/CRAM files. This information can be generated using paragraph/idxdepth. More information can be found here: https://github.com/Illumina/paragraph#sample-manifest

#2 tuple

`meta2` map	Groovy Map containing sample information for the FASTA file e.g. [ id:'test', single_end:false ]
`fasta` file	The reference FASTA file used to generate the VCF and BAM/CRAM files `*.{fa,fasta,fna}`

#3 tuple

`meta3` map	Groovy Map containing sample information for the FASTA index file e.g. [ id:'test', single_end:false ]
`fasta_fai` file	The index of the reference FASTA file `*.fai`

Output 3 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	The genotyped VCF file in BGZIP format `*.vcf.gz`

#2 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.json.gz` file	The genotyped JSON file in GZIP format `*.json.gz`

#3 versions

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

Tool	Description	Homepage
paragraph	Graph realignment tools for structural variants	https://github.com/Illumina/paragraph

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:01:23 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fparagraph%2Fmultigrmpy/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/paragraph/multigrmpy/blobs/sha256:75ae1b5ff55d83b97e0dac5e6a0519bd57e7b8e7f81f87c1e2afb873d67fbbe1
Size	3.5 KB
Checksum	sha256:75ae1b5ff55d83b97e0dac5e6a0519bd57e7b8e7f81f87c1e2afb873d67fbbe1
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:01:23 (UTC)		1	3.5 KB	-