feat: add vcontact3/run module

modules/nf-core/vcontact3/run/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::vcontact3=3.1.6=pyhdfd78af_0

modules/nf-core/vcontact3/run/main.nf

@@ -0,0 +1,38 @@
+process VCONTACT3_RUN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularityOptions ?
+        'docker://quay.io/biocontainers/vcontact3:3.1.6--pyhdfd78af_0' :
+        'quay.io/biocontainers/vcontact3:3.1.6--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(genomes)
+
+    output:
+    tuple val(meta), path("vcontact3_output/"), emit: results
+    tuple val("${task.process}"), val('vcontact3'), val('3.1.6'), emit: versions_vcontact3, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    vcontact3 run \\
+        -n ${genomes.join(' ')} \\
+        -o vcontact3_output/ \\
+        --threads ${task.cpus} \\
+        ${args}
+    """
+
+    stub:
+    """
+    mkdir -p vcontact3_output/
+    touch vcontact3_output/clusters.csv
+    touch vcontact3_output/merged_df.csv
+    touch vcontact3_output/vContact_contig_id.txt
+    """
+}

modules/nf-core/vcontact3/run/meta.yml

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+name: vcontact3_run
+description: Cluster viral genomes using protein-level homology comparison
+keywords:
+  - virology
+  - clustering
+  - metagenomics
+  - virus
+  - homology
+tools:
+  - vcontact3:
+      description: Automated host-to-phage gene-level similarity searching
+      homepage: https://bitbucket.org/MAVERICLab/vcontact3
+      documentation: https://vcontact3.readthedocs.io/en/latest/
+      tool_dev_url: https://bitbucket.org/MAVERICLab/vcontact3
+      licence:
+        - GPL-3.0-or-later
+      doi: 10.1186/s13059-019-1879-9
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: Groovy map containing sample metadata
+    - genomes:
+        type: file
+        description: Input FASTA or GenBank files with viral sequences
+        pattern: "*.{fasta,fa,faa,gbk,gb}"
+        ontologies: []
+output:
+  results:
+    - - meta:
+          type: map
+          description: Groovy map with sample metadata
+      - vcontact3_output/:
+          type: directory
+          description: VCONTACT3 output directory containing clustering results
+          pattern: "vcontact3_output/"
+  versions_vcontact3:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - vcontact3:
+          type: string
+          description: The name of the tool
+      - 3.1.6:
+          type: string
+          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
+      - 3.1.6:
+          type: string
+          description: The expression to obtain the version of the tool
+authors:
+  - "@JP-Bro"
+maintainers:
+  - "@JP-Bro"

modules/nf-core/vcontact3/run/tests/main.nf.test

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+nextflow_process {
+    name "Test Process VCONTACT3_RUN"
+    script "../main.nf"
+    process "VCONTACT3_RUN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vcontact3"
+    tag "vcontact3/run"
+
+    test("vcontact3_run - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+        }
+    }
+
+    test("vcontact3_run - real") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert path(process.out.results[0][1]).exists()
+        }
+    }
+}

modules/nf-core/vcontact3/run/tests/main.nf.test.snap

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+{
+    "vcontact3_run - stub": {
+        "results": [
+            [
+                {
+                    "id": "test"
+                },
+                [
+                    "vcontact3_output"
+                ]
+            ]
+        ],
+        "versions_vcontact3": [
+            [
+                "VCONTACT3_RUN",
+                "vcontact3",
+                "3.1.6"
+            ]
+        ]
+    }
+}