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

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

The Reporter module is responsible for generating a report with genotype-specific expert-reviewed drug prescribing recommendations for clinical decision support.

pharmcat report PGx

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ramsainanduri

Maintainers: @ramsainanduri

Summary

The Reporter module is responsible for generating a report with genotype-specific expert-reviewed drug prescribing recommendations for clinical decision support.

Get started

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

include { PHARMCAT_REPORTER } from 'nf-core/pharmcat/reporter'

License

MIT License

Process

`Name`	`PHARMCAT_REPORTER`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', name:'test_sample' ]`
`phenotypes` file	The vcf file to be inspected `*.json`

Output 4 channels

#1 report_tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', name:'test_sample' ]`
`*.report.tsv` file	Tab separated output from the reporter module of PharmCAT `*.report.tsv`

#2 report_html tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', name:'test_sample' ]`
`*.report.html` file	HTML output from the reporter module of PharmCAT `*.report.html`

#3 report_json tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', name:'test_sample' ]`
`*.report.json` file	Json output from the reporter module of PharmCAT `*.report.json`

#4 versions_pharmcat tuple

`${task.process}` string	The name of the process
`pharmcat` string	The name of the tool
`pharmcat --version \| cut -f2 -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 19:02:10 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpharmcat%2Freporter/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/pharmcat/reporter/blobs/sha256:7503c91868e5cb6d602b68c752f5aebe5748b2446744611a4ea6220f9cdbcdd5
Size	3.2 KB
Checksum	sha256:7503c91868e5cb6d602b68c752f5aebe5748b2446744611a4ea6220f9cdbcdd5
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:02:10 (UTC)		1	3.2 KB	-