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nf-core/wittyer @ 0.0.0-0c7146d

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.

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

  2. Download the latest release.

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

  3. Uncompress the released package.

    tar -xvf <VERSION>.tar.gz

  4. Change to the uncompressed directory.

  5. Build docker image using provided Dockerfile.

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

  6. 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>

  7. 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 0.0.0-0c7146d
Commit ID 3fc6d40d163d89ae44d40a00b9017d5a9df5170e
Release Date 08 Apr 2026 19:48:04 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fwittyer/0.0.0-0c7146d/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/wittyer/blobs/sha256:129e2d06273f7d73cc25bf4761c3c69fa65c3538dec4b631feb653f1c3569e49
Size 4.3 KB
Checksum sha256:129e2d06273f7d73cc25bf4761c3c69fa65c3538dec4b631feb653f1c3569e49
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