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feat: civicpy/annotate module
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‎modules/nf-core/civicpy/annotate/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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- nodefaults
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dependencies:
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- "bioconda::civicpy=5.2.0"

‎modules/nf-core/civicpy/annotate/main.nf‎

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process CIVICPY_ANNOTATE {
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tag "${meta.id}"
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'oras://community.wave.seqera.io/library/civicpy:5.2.0--8e87770abedd45a6'
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: 'community.wave.seqera.io/library/pip_backports-datetime-fromisoformat_civicpy:fe223053d0547acf' }"
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input:
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tuple val(meta), path(vcf), path(tbi)
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val annotation_genome_version
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output:
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tuple val(meta), path("*.vcf"), emit: vcf
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tuple val("${task.process}"), val('civicpy'), eval("civicpy --version | sed 's/.*version //'"), topic: versions, emit: versions_civicpy
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}.civic"
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"""
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export CIVICPY_CACHE_FILE=\$PWD/.civicpy
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civicpy annotate-vcf \\
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--input-vcf ${vcf} \\
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--output-vcf ${prefix}.vcf \\
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--reference ${annotation_genome_version} \\
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${args}
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}.civic"
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"""
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touch ${prefix}.vcf
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"""
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}

‎modules/nf-core/civicpy/annotate/meta.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "civicpy_annotate"
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description: A python client and analysis toolkit for the Clinical Interpretations of Variants in Cancer (CIViC) knowledgebase
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keywords:
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- clinical interpretation
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- variant annotation
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- genetic variation analysis
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- genomics
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tools:
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- "civicpy":
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description: "CIViC variant knowledgebase analysis toolkit."
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homepage: "https://docs.civicpy.org/en/latest/"
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documentation: "https://docs.civicpy.org/en/latest/"
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tool_dev_url: "https://github.com/griffithlab/civicpy"
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doi: "10.1200/CCI.19.00127"
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licence: ["MIT"]
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identifier: biotools:CIViCpy
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1', single_end:false ]`
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- vcf:
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type: file
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description: Sorted and indexed VCF file
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pattern: "*.{vcf}"
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ontologies:
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- edam: "http://edamontology.org/format_3016"
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- tbi:
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type: file
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description: Tabix index for the input VCF
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pattern: "*.tbi"
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- annotation_genome_version:
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type: string
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description: Reference genome version passed to civicpy (e.g. GRCh38)
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output:
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vcf:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1', single_end:false ]`
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- "*.vcf":
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type: file
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description: Annotated VCF file
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pattern: "*.vcf"
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ontologies:
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- edam: "http://edamontology.org/format_3016"
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versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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authors:
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- "@emmcauley"
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maintainers:
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- "@emmcauley"

‎modules/nf-core/civicpy/annotate/tests/main.nf.test‎

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nextflow_process {
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name "Test Process CIVICPY_ANNOTATE"
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script "../main.nf"
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process "CIVICPY_ANNOTATE"
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config "./nextflow.config"
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tag "modules"
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tag "modules_nfcore"
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tag "civicpy"
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tag "civicpy/annotate"
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test("homo_sapiens - vcf - GRCh38") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test_sample' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
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]
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input[1] = 'GRCh38'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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path(process.out.vcf[0][1]).vcf.variantsMD5,
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process.out.versions_civicpy
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).match() }
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)
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}
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}
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test("homo_sapiens - vcf - GRCh37") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test_sample' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
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]
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input[1] = 'GRCh37'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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path(process.out.vcf[0][1]).vcf.variantsMD5,
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process.out.versions_civicpy
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).match() }
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)
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}
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}
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test("homo_sapiens - vcf - GRCh38 - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id:'test_sample' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
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]
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input[1] = 'GRCh38'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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file(process.out.vcf[0][1]).name,
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process.out.versions_civicpy
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).match() }
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)
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}
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}
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}

‎modules/nf-core/civicpy/annotate/tests/main.nf.test.snap‎

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{
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"homo_sapiens - vcf - GRCh38 - stub": {
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"content": [
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"test_sample.civic.vcf",
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[
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[
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"CIVICPY_ANNOTATE",
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"civicpy",
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"5.2.0"
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]
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]
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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},
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"timestamp": "2026-03-26T17:38:23.86228"
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},
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"homo_sapiens - vcf - GRCh37": {
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"content": [
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"bf3fe04101ac5b192de625ebf9a4324f",
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[
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[
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"CIVICPY_ANNOTATE",
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"civicpy",
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"5.2.0"
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]
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]
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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},
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"timestamp": "2026-03-27T11:16:21.699688"
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},
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"homo_sapiens - vcf - GRCh38": {
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"content": [
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"bf3fe04101ac5b192de625ebf9a4324f",
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[
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[
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"CIVICPY_ANNOTATE",
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"civicpy",
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"5.2.0"
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]
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]
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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},
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"timestamp": "2026-03-27T11:15:57.673023"
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}
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}

‎modules/nf-core/civicpy/annotate/tests/nextflow.config‎

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process {
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withName: CIVICPY_ANNOTATE {
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ext.args = '--include-status accepted'
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}
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}

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