Nextflow Registry | nf-core/civicpy/annotate@0.0.0-eac429d

nf-core/civicpy/annotate @ 0.0.0-eac429d

A python client and analysis toolkit to annotate variants with information from the Clinical Interpretations of Variants in Cancer (CIViC) knowledgebase

clinical interpretation variant annotation genetic variation analysis genomics

Latest version: 0.0.0-eac429d

Total downloads: 0

Source: nf-core/modules

Authors: @emmcauley

Maintainers: @emmcauley

Summary

A python client and analysis toolkit to annotate variants with information from the Clinical Interpretations of Variants in Cancer (CIViC) knowledgebase

Get started

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

include { CIVICPY_ANNOTATE } from 'nf-core/civicpy/annotate'

License

MIT License

Process

`Name`	`CIVICPY_ANNOTATE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`vcf` file	Sorted and indexed VCF file `*.{vcf}`
`tbi` file	Tabix index for the input VCF `*.tbi`

`annotation_genome_version` string	Reference genome version passed to civicpy (e.g. GRCh38)

`cache` file	Optional civicpy cache file (.pkl). If not provided, civicpy will download and cache data locally. `.pkl`

Output 3 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.vcf.gz` file	Annotated bgzipped VCF file `*.vcf.gz`

#2 versions_htslib tuple

`${task.process}` string	The name of the process
`htslib` string	The name of the tool
`bgzip --version 2>&1 \| head -1 \| sed 's/bgzip (htslib) //'` eval	The expression to obtain the version of the tool

#3 versions_civicpy tuple

`${task.process}` string	The name of the process
`civicpy` string	The name of the tool
`civicpy --version \| sed 's/.*version //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
civicpy	CIViC variant knowledgebase analysis toolkit.	https://docs.civicpy.org/en/latest/

Version	0.0.0-eac429d
Commit ID	eac429d4c67ac5114ce7d4287d460d8f05fd9fab
Release Date	20 May 2026 15:01:15 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcivicpy%2Fannotate/0.0.0-eac429d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/civicpy/annotate/blobs/sha256:8e1967bd512200959a240050af920ccdf2aa63f5a77c6216b6499596ce3e8adb
Size	3.0 KB
Checksum	sha256:8e1967bd512200959a240050af920ccdf2aa63f5a77c6216b6499596ce3e8adb
Downloads	0

Version	Date	Status	Downloads	Size	Diff
0.0.0-eac429d	20 May 2026 15:01:15 (UTC)		0	3.0 KB	-