Nextflow Registry | nf-core/vardictjava@0.0.0-6c4ed3a

nf-core/vardictjava @ 0.0.0-6c4ed3a

The Java port of the VarDict variant caller

variant calling vcf bam snv sv

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

The Java port of the VarDict variant caller

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

include { VARDICTJAVA } from 'nf-core/vardictjava'

MIT License

Process

`Name`	`VARDICTJAVA`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bams` file	One or two BAM files. Supply two BAM files to run Vardict in paired mode. `*.bam`
`bais` file	Index/indices of the BAM file(s) `*.bai`
`bed` file	BED with the regions of interest `*.bed`

#2 tuple

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

#3 tuple

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

Output 4 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	VCF file output `*.vcf.gz`

#2 versions_htslib tuple

`${task.process}` string	The name of the process
`htslib` string	The name of the tool
`tabix -h 2>&1 \| sed -n '2s/Version: *//p'` eval	The expression to obtain the version of the tool

#3 versions_vardictjava tuple

`${task.process}` string	The name of the process
`vardict-java` string	The name of the tool
`realpath \$( command -v vardict-java ) \| sed 's/.java-//;s/-.//'` eval	The expression to obtain the version of the tool

#4 versions_var2vcfvalid tuple

`${task.process}` string	The name of the process
`var2vcf_valid.pl` string	The name of the tool
`var2vcf_valid.pl -h \| sed '2!d;s/.* //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
vardictjava	Java port of the VarDict variant discovery program	https://github.com/AstraZeneca-NGS/VarDictJava

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:51:38 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fvardictjava/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/vardictjava/blobs/sha256:787fa229880abbd3ff66cf7d04bcf1146a63ce2c321887c10b9f7b5420bdcd85
Size	3.2 KB
Checksum	sha256:787fa229880abbd3ff66cf7d04bcf1146a63ce2c321887c10b9f7b5420bdcd85
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