nf-core/pharmcat/phenotyper @ 0.0.0-0c7146d
Summary
The PharmCAT Phenotyper is a core module of the Pharmacogenomics Clinical Annotation Tool that translates patient diplotypes into specific, actionable metabolizer phenotypes (e.g., Poor Metabolizer). It operates by analyzing the JSON output from the Named Allele Matcher, mapping these results to established clinical guidelines (such as CPIC) to predict drug response.
Get started
Add the following snippet to your workflow script to include this module.
include { PHARMCAT_PHENOTYPER } from 'nf-core/pharmcat/phenotyper'
License
MIT License
Name
|
PHARMCAT_PHENOTYPER |
|---|
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
match_json
file
|
The Json output from the matcher module of pharmcat *.json
|
outside_match_tsv
file
|
Tab seperated file containing diplotypes calls from other callers *.tsv
|
phenotyper_json
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.phenotype.json
file
|
Json output from the phenotyper module of PharmCAT *.phenotype.json
|
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 19:02:08 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpharmcat%2Fphenotyper/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/pharmcat/phenotyper/blobs/sha256:37b3964c87f59c9b35d8ed45636635b4b3f7dc134c0dae35af120fb5a4dc3774 |
| Size | 3.0 KB |
| Checksum | sha256:37b3964c87f59c9b35d8ed45636635b4b3f7dc134c0dae35af120fb5a4dc3774 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:02:08 (UTC) | 1 | 3.0 KB | - |