feat(vcontact3): add vcontact3/prepareddatabases module

nf-core/vcontact3/prepareddatabases/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
+dependencies:
+  - "bioconda::vcontact3=3.1.6"

nf-core/vcontact3/prepareddatabases/main.nf

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+process VCONTACT3_PREPAREDDATABASES {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vcontact3:3.1.6--py310h4b81fae_0':
+        'quay.io/biocontainers/vcontact3:3.1.6--py310h4b81fae_0' }"
+
+    input:
+    tuple val(meta), val(db_version)
+
+    output:
+    tuple val(meta), path ("${prefix}/"), emit: database
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    """
+    vcontact3 prepare_databases \\
+        --get-version "${db_version}" \\
+        --set-location "${prefix}"  \\
+        $args
+
+    cat <<EOF > versions.yml
+    "${task.process}":
+        vcontact3: \$(vcontact3 --version 2>&1 | sed 's/vcontact3 //g')
+    EOF
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p "${prefix}"
+    touch "${prefix}/version.json"
+    touch ${prefix}/stub_database.db
+
+    cat <<EOF > versions.yml
+    "${task.process}":
+        vcontact3: 3.1.6
+    EOF
+    """
+}

nf-core/vcontact3/prepareddatabases/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+# # TODO nf-core: Add a description of the module and list keywords
+name: "vcontact3_prepareddatabases"
+description: write your description here
+keywords:
+- sort
+- example
+- genomics
+tools:
+## TODO nf-core: Add a description and other details for the software below
+- "vcontact3":
+    description: "Viral Contig Automatic Clustering and Taxonomy"
+    homepage: "https://bitbucket.org/MAVERICLab/vcontact3/src/master/README.md"
+    documentation: "https://bitbucket.org/MAVERICLab/vcontact3/src/master/README.md"
+    tool_dev_url: "None"
+    doi: ""
+    licence: ['GPL v3']
+    identifier: null
+
+input:
+  ### TODO nf-core: Add a description of all of the variables used as input
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+      ontologies:
+      - edam: "http://edamontology.org/format_2572"     # BAM
+      - edam: "http://edamontology.org/format_2573"     # CRAM
+      - edam: "http://edamontology.org/format_3462"     # SAM
+
+output:
+  ### TODO nf-core: Add a description of all of the variables used as output
+  bam:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - "*.bam":
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+        - edam: "http://edamontology.org/format_2572"     # BAM
+        - edam: "http://edamontology.org/format_2573"     # CRAM
+        - edam: "http://edamontology.org/format_3462"     # SAM
+  versions_vcontact3:
+  - - "${task.process}":
+        type: string
+        description: The name of the process
+    - "vcontact3":
+        type: string
+        description: The name of the tool
+    - "vcontact3 --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
+    - vcontact3:
+        type: string
+        description: The name of the tool
+    - vcontact3 --version:
+        type: eval
+        description: The expression to obtain the version of the tool
+authors:
+- "@olawal1001"
+maintainers:
+- "@olawal1001"

nf-core/vcontact3/prepareddatabases/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process VCONTACT3_PREPAREDDATABASES"
+    script "../main.nf"
+    process "VCONTACT3_PREPAREDDATABASES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vcontact3"
+    tag "vcontact3/prepareddatabases"
+
+    test("vcontact3_prepare_databases - latest_version") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    'latest'
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            def meta  = process.out.database.get(0).get(0)
+            def dbDir = process.out.database.get(0).get(1)
+
+            assertAll(
+                { assert meta.id == 'test' },
+                { assert path(dbDir).exists() },
+                { assert snapshot(process.out.versions).match("real_versions") }
+            )
+        }
+    }
+
+    test("vcontact3_prepare_databases - latest_version - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    'latest'
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            def meta   = process.out.database.get(0).get(0)
+            def dbDir  = process.out.database.get(0).get(1)
+
+            assertAll(
+                { assert meta.id == 'test' },
+                { assert path(dbDir).exists() },
+                { assert path("${dbDir}/version.json").exists() },
+                { assert path("${dbDir}/stub_database.db").exists() },
+                { assert snapshot(process.out.versions).match("stub_versions") }
+            )
+        }
+    }
+}

nf-core/vcontact3/prepareddatabases/tests/main.nf.test.snap

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+{
+    "real_versions": {
+        "content": [
+            [
+                "versions.yml:md5,00d4049fe50f682cda026d348995df3d"
+            ]
+        ],
+        "timestamp": "2026-05-20T17:12:33.278397904",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    },
+    "stub_versions": {
+        "content": [
+            [
+                "versions.yml:md5,eef00dbab0560cd5f7e06c11bafe33de"
+            ]
+        ],
+        "timestamp": "2026-05-19T18:30:59.489287902",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    },
+    "sarscov2 - database_and_fasta- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "stub_database.db:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,eef00dbab0560cd5f7e06c11bafe33de"
+                ],
+                "database": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "stub_database.db:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,eef00dbab0560cd5f7e06c11bafe33de"
+                ]
+            }
+        ],
+        "timestamp": "2026-05-18T18:23:58.3091529",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    }
+}