Nextflow Registry | nf-core/delly/call@0.0.0-0c7146d

nf-core/delly/call @ 0.0.0-0c7146d

Call structural variants

genome structural variants bcf

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @projectoriented @nvnieuwk

Maintainers: @projectoriented @nvnieuwk

Call structural variants

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

include { DELLY_CALL } from 'nf-core/delly/call'

MIT License

Process

`Name`	`DELLY_CALL`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked `*.{bam,cram}`
`input_index` file	Index of the BAM/CRAM file `*.{bai,crai}`
`vcf` file	A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped `*.{vcf.gz,bcf}`
`vcf_index` file	The index of the BCF/VCF file `*.{tbi,csi}`
`exclude_bed` file	An optional bed file containing regions to exclude from the called VCF `*.bed`

#2 tuple

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

#3 tuple

`meta3` map	Groovy Map containing fasta index information e.g. [ id:'test', single_end:false ]
`fai` file	Index of reference fasta file to identify split-reads `*.fai`

`suffix` string	A flag to specify whether the output should be in BCF or VCF format

Output 3 channels

#1 bcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{bcf,vcf.gz}` file	Called variants in BCF/VCF format. Set suffix to either "bcf" or "vcf" to define the output type `*.{bcf,vcf.gz}`

#2 csi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{csi,tbi}` file	A generated csi index that matches the bcf output (not generated for vcf files) `*.{bcf.csi}`

#3 versions_delly tuple

`${task.process}` string	The name of the process
`delly` string	The name of the tool
`delly --version \|& sed -n '1s/Delly version: *v//p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
delly	Structural variant discovery by integrated paired-end and split-read analysis	https://github.com/dellytools/delly

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:35:54 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fdelly%2Fcall/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/delly/call/blobs/sha256:4af118d095a8186f260d5183882c931d5a64f77ab5149873716635c4691dfe6f
Size	3.5 KB
Checksum	sha256:4af118d095a8186f260d5183882c931d5a64f77ab5149873716635c4691dfe6f
Downloads	1

Version