Nextflow Registry | nf-core/paragraph/multigrmpy@0.0.0-6c4ed3a

nf-core/paragraph/multigrmpy @ 0.0.0-6c4ed3a

Genotype structural variants using paragraph and grmpy

vcf json structural variants graphs genotyping

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:35:08 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fparagraph%2Fmultigrmpy/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/paragraph/multigrmpy/blobs/sha256:b010ed9bd97b659e9b6717ada51354a932dfd492c20fc2ad2fb464c3cee40778
Size	3.5 KB
Checksum	sha256:b010ed9bd97b659e9b6717ada51354a932dfd492c20fc2ad2fb464c3cee40778
Downloads	4

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:35:08 (UTC)	4	3.5 KB
0.0.0-3fc6d40	22 Apr 2026 15:25:16 (UTC)	3	3.5 KB
0.0.0-0c7146d