feat: civicpy/annotate module

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

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - "bioconda::civicpy=5.3.0"
+  - "bioconda::htslib=1.21"

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

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+process CIVICPY_ANNOTATE {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/civicpy:5.3.0--pyhdfd78af_0'
+        : 'biocontainers/civicpy:5.3.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+    val annotation_genome_version
+    path cache
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    tuple val("${task.process}"), val('civicpy'), eval("civicpy --version | sed 's/.*version //'"), topic: versions, emit: versions_civicpy
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args   ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    if ("${vcf}" == "${prefix}.vcf.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    export CIVICPY_CACHE_FILE=\$PWD/${cache}
+
+    civicpy annotate-vcf \\
+        --input-vcf ${vcf} \\
+        --output-vcf ${prefix}.vcf \\
+        --reference ${annotation_genome_version} \\
+        ${args}
+
+    bgzip ${prefix}.vcf
+    """
+
+    stub:
+    def args   = task.ext.args   ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    if ("${vcf}" == "${prefix}.vcf.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    echo "" | gzip > ${prefix}.vcf.gz
+    """
+}

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

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+name: "civicpy_annotate"
+description: A python client and analysis toolkit to annotate variants with
+  information from the Clinical Interpretations of Variants in Cancer (CIViC)
+  knowledgebase
+keywords:
+  - clinical interpretation
+  - variant annotation
+  - genetic variation analysis
+  - genomics
+tools:
+  - "civicpy":
+      description: "CIViC variant knowledgebase analysis toolkit."
+      homepage: "https://docs.civicpy.org/en/latest/"
+      documentation: "https://docs.civicpy.org/en/latest/"
+      tool_dev_url: "https://github.com/griffithlab/civicpy"
+      doi: "10.1200/CCI.19.00127"
+      licence:
+        - "MIT"
+      identifier: biotools:CIViCpy
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - vcf:
+        type: file
+        description: Sorted and indexed VCF file
+        pattern: "*.{vcf}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016"
+    - tbi:
+        type: file
+        description: Tabix index for the input VCF
+        pattern: "*.tbi"
+        ontologies: []
+  - annotation_genome_version:
+      type: string
+      description: Reference genome version passed to civicpy (e.g. GRCh38)
+output:
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.vcf.gz":
+          type: file
+          description: Annotated bgzipped VCF file
+          pattern: "*.vcf.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_3016"
+            - edam: http://edamontology.org/format_3989
+  versions_civicpy:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - civicpy:
+          type: string
+          description: The name of the tool
+      - civicpy --version | sed 's/.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - civicpy:
+          type: string
+          description: The name of the tool
+      - civicpy --version | sed 's/.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@emmcauley"
+maintainers:
+  - "@emmcauley"

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

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+nextflow_process {
+
+    name "Test Process CIVICPY_ANNOTATE"
+    script "../main.nf"
+    process "CIVICPY_ANNOTATE"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "civicpy"
+    tag "civicpy/annotate"
+
+    test("homo_sapiens - vcf - GRCh38") {
+
+        when {
+            params {
+                module_args = '--include-status accepted'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test_sample' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz',    checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = 'GRCh38'
+                input[2] = [] // no cache
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.vcf[0][1]).vcf.variantsMD5,
+                    process.out.versions_civicpy
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - vcf - GRCh37") {
+
+        when {
+            params {
+                module_args = '--include-status accepted'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test_sample' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz',    checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = 'GRCh37'
+                input[2] = [] // no cache
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.vcf[0][1]).vcf.variantsMD5,
+                    process.out.versions_civicpy
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - vcf - GRCh38 - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                module_args = '--include-status accepted'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test_sample' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz',    checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = 'GRCh38'
+                input[2] = [] // no cache
+                """
+            }
+        }
+
+        then {
+            assert snapshot(sanitizeOutput(process.out)).match()
+        }
+
+    }
+
+}

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

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+{
+    "homo_sapiens - vcf - GRCh38 - stub": {
+        "content": [
+            {
+                "vcf": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        "/Users/erin/git/fg/nf-core-modules/.nf-test/tests/68c278fdc09fc81e903baebccd095f9b/work/67/5f3e6d98571cd26509b0fc94a4804a/test_sample.civic.vcf.gz"
+                    ]
+                ],
+                "versions_civicpy": [
+                    [
+                        "CIVICPY_ANNOTATE",
+                        "civicpy",
+                        ""
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-04-14T12:22:14.319968"
+    },
+    "homo_sapiens - vcf - GRCh37": {
+        "content": [
+            "bf3fe04101ac5b192de625ebf9a4324f",
+            [
+                [
+                    "CIVICPY_ANNOTATE",
+                    "civicpy",
+                    "5.2.0"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-03-27T11:16:21.699688"
+    },
+    "homo_sapiens - vcf - GRCh38": {
+        "content": [
+            "bf3fe04101ac5b192de625ebf9a4324f",
+            [
+                [
+                    "CIVICPY_ANNOTATE",
+                    "civicpy",
+                    "5.2.0"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-03-27T11:15:57.673023"
+    }
+}

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

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+process {
+    withName: CIVICPY_ANNOTATE {
+        ext.args = params.module_args
+    }
+}