nf-core/wittyer @ 0.0.0-3fc6d40

A large variant benchmarking tool analogous to hap.py for small variants.

structural-variants benchmarking vcf

Latest version: 0.0.0-3fc6d40

Total downloads: 6

Source: nf-core/modules

Authors: @famosab

Maintainers: @famosab

Updating the docker container and making a new module release

witty.er is a commercial tool from Illumina. The container provided for the witty.er nf-core module is not provided nor supported by Illumina. Updating the witty.er versions in the container and pushing the update to Dockerhub needs to be done manually. NOTE: an updated version of Dockerfile than the official one in github is used to build nf-core/wittyer:0.5.2, which is inserted here ./Dockerfile.

Navigate to the witty.er github repository. - witty.er

Download the latest release.

wget https://github.com/Illumina/witty.er/archive/refs/tags/<VERSION>.tar.gz

Uncompress the released package.
```
tar -xvf <VERSION>.tar.gz
```
Change to the uncompressed directory.

Build docker image using provided Dockerfile.

docker build -t wittyer:<VERSION> --platform linux/amd64 .

Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
```
docker tag wittyer:<VERSION> quay.io/nf-core/wittyer:<VERSION>
docker push quay.io/nf-core/wittyer:<VERSION>
```
Make the image public.

Process

`Name`	`WITTYER`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`query_vcf` file	A VCF with called variants to benchmark against the standard `*.{vcf}`
`truth_vcf` file	A standard VCF to compare against `*.{vcf}`
`bed` file	A BED file specifying regions to be included in the analysis (optional) `*.bed`
`wittyer_config` file	Config file in json format used to specify per variant type settings. Used in place of include bed arguments. (optional) `*.json`

Output 4 channels

#1 report tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.json` file	Detailed per-sample-pair, per-svtype, per-bin stats `*.json`

#2 bench_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.vcf.gz` file	Updated query and truth entries merged into one file `*.vcf.gz`

#3 bench_vcf_tbi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.vcf.gz.tbi` file	Index of merged query and truth entries VCF file `*.vcf.gz.tbi`

#4 versions_wittyer tuple

`${task.process}` string	The process the versions were collected from
`wittyer` string	The name of the tool
`dotnet /opt/Wittyer/Wittyer.dll --version \| sed '1!d ; s/witty.er //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
wittyer	Illumina tool for large variant benchmarking	https://github.com/Illumina/witty.er

Version	0.0.0-3fc6d40
Commit ID	3fc6d40d163d89ae44d40a00b9017d5a9df5170e
Release Date	22 Apr 2026 15:36:59 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fwittyer/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/wittyer/blobs/sha256:c4e329f5036b19618394a2659ed33cdbc300544877156641e9bcfc21cdedd9b8
Size	4.3 KB
Checksum	sha256:c4e329f5036b19618394a2659ed33cdbc300544877156641e9bcfc21cdedd9b8
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-3fc6d40	22 Apr 2026 15:36:59 (UTC)		3	4.3 KB
0.0.0-0c7146d	08 Apr 2026 19:48:04 (UTC)		3	4.3 KB