Nextflow Registry | nf-core/gridss/generateponbedpe@0.0.0-6c4ed3a

nf-core/gridss/generateponbedpe @ 0.0.0-6c4ed3a

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

gridss structural variants bedpe bed vcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 12

Source: nf-core/modules

Authors: @kubranarci

Maintainers: @famosab

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

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

include { GRIDSS_GENERATEPONBEDPE } from 'nf-core/gridss/generateponbedpe'

MIT License

Process

`Name`	`GRIDSS_GENERATEPONBEDPE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`vcf` file	GRIDSS generated vcf file `*.vcf`
`bedpe` file	GRIDSS generated bedpe file `*.bedpe`
`bed` file	GRIDSS generated bed file `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test']
`fasta` file	The reference fasta `*.{fa,fna,fasta}`

#3 tuple

`meta3` map	Groovy Map containing reference fai information e.g. [ id:'test']
`fai` file	The index of the reference fasta `*.fai`

#4 tuple

`meta4` map	Groovy Map containing bwa generated index information e.g. [ id:'test']
`bwa_index` directory	OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step

Output 3 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.bed` file	GRIDSS generated breakpoint pon bed file `*.bed`

#2 bedpe tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.bedpe` file	GRIDSS generated breakpoint pon bedpe file `*.bedpe`

#3 versions_gridss tuple

`${task.process}` string	The process
`gridss` string	The tool name
`GeneratePonBedpe --version 2>&1 \| sed 's/-gridss//'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gridss	GRIDSS: the Genomic Rearrangement IDentification Software Suite	n/a

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:22:01 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgridss%2Fgenerateponbedpe/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gridss/generateponbedpe/blobs/sha256:18073850042e3fa4e85d1dc6887c75ca5f150db7b00f4adc1e6af6b62170a932
Size	2.9 KB
Checksum	sha256:18073850042e3fa4e85d1dc6887c75ca5f150db7b00f4adc1e6af6b62170a932
Downloads	2

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:22:01 (UTC)		2	2.9 KB