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nf-core/pharmcat/vcfpreprocessor @ 0.0.0-6c4ed3a

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: 0.0.0-6c4ed3a
Total downloads: 11
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 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:35:43 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fpharmcat%2Fvcfpreprocessor/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pharmcat/vcfpreprocessor/blobs/sha256:299e4c7e5cb4a7ab084373a9724e8a1948cbd5f259593ab987c2767c21e3e7e6