Nextflow Registry | nf-core/pharmcat/vcfpreprocessor@0.0.0-0c7146d

nf-core/pharmcat/vcfpreprocessor @ 0.0.0-0c7146d

The PharmCAT VCF Preprocessor is a script that can pre-process VCF files for PharmCAT to make sure the VCF file complies with PharmCAT's VCF Requirements

preprocessing vcf phamrcat

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ramsainanduri

Maintainers: @ramsainanduri

Summary

The PharmCAT VCF Preprocessor is a script that can pre-process VCF files for PharmCAT to make sure the VCF file complies with PharmCAT's VCF Requirements

Get started

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

include { PHARMCAT_VCFPREPROCESSOR } from 'nf-core/pharmcat/vcfpreprocessor'

License

MIT License

Process

`Name`	`PHARMCAT_VCFPREPROCESSOR`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', name:'test_sample' ]`
`vcf_gz` file	The vcf file to be inspected `*.vcf.gz`
`vcf_index` file	The tbi/csi file to be inspected `*.{tbi,csi}`

#2 tuple

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

#3 tuple

`meta3` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`fai` file	Genome index file `*.{fai,fai.gz}`

#4 tuple

`meta4` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`pharmcat_positions` file	Pharmcat positions vcf `*.vcf.{gz,bgz}`
`pharmcat_positions_index` file	Pharmcat positions vcf index file `*.{tbi,csi}`

#5 tuple

`meta5` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`pharmcat_uniallelic_positions` file	Pharmcat uniallelic positions vcf `*.vcf.{gz,bgz}`
`pharmcat_uniallelic_positions_index` file	Pharmcat uniallelic positions vcf index file `*.{tbi,csi}`

Output 3 channels

#1 missing_pgx_var tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', name:'test_sample' ]`
`*.missing_pgx_var.vcf` file	Missing position in PGX VCF file `*.missing_pgx_var.vcf`

#2 preprocessed_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', name:'test_sample' ]`
`*.preprocessed.vcf.bgz` file	Preprocessed vcf file `*.preprocessed.vcf.bgz`

#3 versions_pharmcat_vcf_preprocessor tuple

`${task.process}` string	The name of the process
`pharmcat_vcf_preprocessor` string	The name of the tool
`pharmcat_vcf_preprocessor --version \| cut -f4 -d ' '` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
pharmcat	PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics tool that analyzes genetic variants to predict drug response and tailor medical treatment to an individual patient’s genetic profile.	https://pharmcat.clinpgx.org/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:02:11 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpharmcat%2Fvcfpreprocessor/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/pharmcat/vcfpreprocessor/blobs/sha256:7e65837ff8dea23dbddad349237c22822db8dd8ff0731402921d346e1ba3700b