nf-core/duphold @ 0.0.0-6c4ed3a
Summary
SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content.
Get started
Add the following snippet to your workflow script to include this module.
include { DUPHOLD } from 'nf-core/duphold'
License
MIT License
Name
|
DUPHOLD |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
alignment_file
file
|
file containing alignments |
alignment_index
file
|
index of alignment file |
sv_variants
file
|
A variants file containing structural variants *.{vcf,bcf}(.gz)?
|
snp_variants
file
|
A variants file containing SNPs *.{vcf,bcf}(.gz)?
|
snp_variants_index
file
|
index of snp variants file |
fasta
file
|
fasta file *.{fa,fasta,fna}
|
|---|
fasta_fai
file
|
Index of fasta file *.fai
|
|---|
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.vcf.gz
file
|
The output VCF *.vcf.gz
|
versions_duphold
tuple
${task.process}
string
|
The name of the process |
|---|---|
duphold
string
|
The name of the tool |
duphold -h | sed -e "s/^version: //;q"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| duphold | SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. | https://github.com/brentp/duphold |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:14:30 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fduphold/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/duphold/blobs/sha256:dafc3edb9dca82010c5c86de095cd7a79ab221aff7508c00ea05cf1334db4f58 |
| Size | 2.9 KB |
| Checksum | sha256:dafc3edb9dca82010c5c86de095cd7a79ab221aff7508c00ea05cf1334db4f58 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:14:30 (UTC) | 3 | 2.9 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:10:34 (UTC) | 3 | 2.9 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:58:02 (UTC) | 2 | 2.9 KB |