Nextflow Registry | nf-core/pypgx/runngspipeline@0.0.0-6c4ed3a

nf-core/pypgx/runngspipeline @ 0.0.0-6c4ed3a

PyPGx pharmacogenomics genotyping pipeline for NGS data.

pypgx pharmacogenetics genotyping

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @jorisvansteenbrugge

Maintainers: @jorisvansteenbrugge

PyPGx pharmacogenomics genotyping pipeline for NGS data.

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

include { PYPGX_RUNNGSPIPELINE } from 'nf-core/pypgx/runngspipeline'

MIT License

Process

`Name`	`PYPGX_RUNNGSPIPELINE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`.
`vcf` file	BGZIP compressed VCF file with SNVs/indels. Output of pypgx/createinputvcf. `*.{vcf.gz}`
`tbi` file	VCF tabix index. `*.{vcf.gz.tbi}`
`coverage` file	ZIP compressed file with depth of coverage information. Output of pypgx/preparedepthofcoverage. Coverage information is only required when running the module on a pharmacogene with known structural variants. `*.{zip}`
`control_stats` file	ZIP compressed file with control statistics. Output of pypgx/computecontrolstatistics. Control statistics are only required when running the module on a pharmacogene with known structural variants.
`pgx_gene` string	Pharmacogene to genotype/phenotype. A list of supported genes is available in the pypgx documentation "https://pypgx.readthedocs.io/en/latest/genes.html"

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`.
`resource_bundle` directory	Path to the pypgx resource bundle (https://github.com/sbslee/pypgx-bundle).

Output 4 channels

#1 results tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*pypgx_output/results.zip` file	Main output file of the pipeline in ZIP format, containing a table with star-alleles per sample and CNV calls where applicable.

#2 cnv_calls tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*pypgx_output/cnv-calls.zip` file	Optional output file in ZIP format, containing CNV calls per sample.

#3 versions_pypgx tuple

`${task.process}` string	The name of the process
`pypgx` string	The name of the tool
`pypgx -v 2>&1 \| grep -oE "[0-9]+\.[0-9]+\.[0-9]+" \| head -1` eval	The expression to obtain the version of the tool

#4 consolidated_variants tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*pypgx_output/consolidated-variants.zip` file	Output file in ZIP format, containing a consolidated (and phased) VCF file.

Tool	Description	Homepage
pypgx	A Python package for pharmacogenomics research	https://pypgx.readthedocs.io/en/latest/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:39:10 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpypgx%2Frunngspipeline/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pypgx/runngspipeline/blobs/sha256:b32c3d58fa9d57f8c59e640edacaffd6afcc6967882bd31e5b7ef4839abfa643
Size	3.7 KB
Checksum	sha256:b32c3d58fa9d57f8c59e640edacaffd6afcc6967882bd31e5b7ef4839abfa643
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4e