nf-core/pharmcat/matcher @ 0.0.0-0c7146d
Summary
The Named Allele Matcher is responsible for calling diplotypes from variant call data. While it is designed to be used in the PharmCAT pipeline, it can also be run independently. The Named Allele Matcher does not currently support structural variants, including gene copy number. If structural variants are detected in the VCF data, it will be ignored and a warning will be issued. If it detects more than the expected number of alleles in the GT column of the VCF, only the first two alleles will be used and a warning will be issued. On haploid chromosomes, only the first allele will be used.
Get started
Add the following snippet to your workflow script to include this module.
include { PHARMCAT_MATCHER } from 'nf-core/pharmcat/matcher'
License
MIT License
Name
|
PHARMCAT_MATCHER |
|---|
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
vcf
file
|
The vcf file to be inspected *.vcf.gz
|
index
file
|
The tbi/csi file to be inspected *.{tbi,csi}
|
genes
list
|
List of genes to be processed |
|---|
matcher_html
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.match.html
file
|
HTML output from the matcher module of PharmCAT *.match.html
|
matcher_json
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.match.json
file
|
Json output from the matcher module of PharmCAT *.match.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 | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:25:04 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fpharmcat%2Fmatcher/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pharmcat/matcher/blobs/sha256:6b2b931575abdc65573936a5678db130186948ed4875a7c494cd90ca8be3ee56 |
| Size | 3.2 KB |
| Checksum | sha256:6b2b931575abdc65573936a5678db130186948ed4875a7c494cd90ca8be3ee56 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:35:39 (UTC) | 3 | 3.2 KB | |
| 0.0.0-5d5b444 | 21 Apr 2026 15:01:12 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:25:04 (UTC) | 4 | 3.2 KB |