Add new module: savana/classify

modules/nf-core/savana/classify/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::savana=1.3.7"

modules/nf-core/savana/classify/main.nf

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+process SAVANA_CLASSIFY {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/savana:1.3.7--pyhdfd78af_0'
+        : 'quay.io/biocontainers/savana:1.3.7--pyhdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("${prefix}.classified.vcf")              , emit: classified_vcf
+    tuple val(meta), path("${prefix}.classified.somatic.vcf")      , emit: somatic_vcf        , optional: true
+    tuple val(meta), path("${prefix}.classified.germline.vcf")     , emit: germline_vcf       , optional: true
+    tuple val(meta), path("${prefix}.classified.somatic.bedpe")    , emit: somatic_bedpe      , optional: true
+    tuple val(meta), path("${prefix}.classified.{strict,lenient}.vcf"), emit: legacy_vcfs     , optional: true
+    tuple val("${task.process}"), val('savana'), eval("python -c \"import importlib.metadata as m; print(m.version('savana'))\""), emit: versions_savana, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = (task.ext.args ?: '').trim()
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    vcf_in="${vcf}"
+    if [[ "${vcf}" == *.gz ]]; then
+        gunzip -c ${vcf} > ${prefix}.input.vcf
+        vcf_in="${prefix}.input.vcf"
+    fi
+
+    savana classify \\
+        --vcf \${vcf_in} \\
+        --output ${prefix}.classified.vcf \\
+        --somatic_output ${prefix}.classified.somatic.vcf \\
+        --threads ${task.cpus ?: 1} \\
+        ${args}
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.classified.vcf
+    touch ${prefix}.classified.somatic.vcf
+    touch ${prefix}.classified.somatic.bedpe
+    touch ${prefix}.classified.strict.vcf
+    touch ${prefix}.classified.lenient.vcf
+    """
+}

modules/nf-core/savana/classify/meta.yml

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+name: "savana_classify"
+description: "Classify structural variants using SAVANA"
+keywords:
+  - classify
+  - structural variants
+  - somatic
+  - germline
+  - genomics
+tools:
+  - "savana":
+      description: "SAVANA: a somatic structural variant caller for long-read data."
+      homepage: "https://github.com/cortes-ciriano-lab/savana"
+      documentation: "https://github.com/cortes-ciriano-lab/savana"
+      tool_dev_url: "https://github.com/cortes-ciriano-lab/savana"
+      doi: "10.1038/s41592-025-02708-0"
+      licence:
+        - "Apache-2.0"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - vcf:
+        type: file
+        description: Input VCF file
+        pattern: "*{.vcf,vcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016"
+          - edam: "http://edamontology.org/format_3615"
+output:
+  classified_vcf:
+    - - meta:
+          type: map
+          description: Sample information
+      - ${prefix}.classified.vcf:
+          type: file
+          description: VCF containing information about variant classification in the INFO field
+          pattern: "*.classified.vcf"
+          ontologies:
+            - edam: "http://edamontology.org/format_3016" # VCF
+  somatic_vcf:
+    - - meta:
+          type: map
+          description: Sample information
+      - ${prefix}.classified.somatic.vcf:
+          type: file
+          description: VCF containing variants classified as somatic
+          pattern: "*.classified.somatic.vcf"
+          ontologies:
+            - edam: "http://edamontology.org/format_3016" # VCF
+  germline_vcf:
+    - - meta:
+          type: map
+          description: Sample information
+      - ${prefix}.classified.germline.vcf:
+          type: file
+          description: VCF containing variants classified as germline
+          pattern: "*.classified.germline.vcf"
+          ontologies:
+            - edam: "http://edamontology.org/format_3016" # VCF
+  somatic_bedpe:
+    - - meta:
+          type: map
+          description: Sample information
+      - ${prefix}.classified.somatic.bedpe:
+          type: file
+          description: Variants classified as somatic in BEDPE format
+          pattern: "*.classified.somatic.bedpe"
+          ontologies:
+            - edam: "http://edamontology.org/format_3003" # BED
+  legacy_vcfs:
+    - - meta:
+          type: map
+          description: Sample information
+      - ${prefix}.classified.{strict,lenient}.vcf:
+          type: file
+          description: Legacy strict/lenient VCFs
+          pattern: "*.classified.{strict,lenient}.vcf"
+          ontologies:
+            - edam: "http://edamontology.org/format_3016" # VCF
+  versions_savana:
+    - - ${task.process}:
+          type: string
+          description: Process name
+      - savana:
+          type: string
+          description: Name of the tool
+      - python -c "import importlib.metadata as m; print(m.version('savana'))":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: Process name
+      - savana:
+          type: string
+          description: Name of the tool
+      - python -c "import importlib.metadata as m; print(m.version('savana'))":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@manascripts"
+maintainers:
+  - "@manascripts"

modules/nf-core/savana/classify/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process SAVANA_CLASSIFY"
+    script "../main.nf"
+    process "SAVANA_CLASSIFY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "savana"
+    tag "savana/classify"
+
+    test("homo_sapiens - vcf") {
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/savana/sv_breakpoints.vcf', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    path(process.out.classified_vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.classified_vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/savana/sv_breakpoints.vcf', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/savana/classify/tests/main.nf.test.snap

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+{
+    "homo_sapiens - vcf": {
+        "content": [
+            "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=29, phased=false, phasedAutodetect=false]",
+            "a03eb2d0fa6a379a43f9ff578fd21607",
+            {
+                "versions_savana": [
+                    [
+                        "SAVANA_CLASSIFY",
+                        "savana",
+                        "1.3.7"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-21T13:56:51.450917438",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.classified.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.classified.somatic.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.classified.somatic.bedpe:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.classified.lenient.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.classified.strict.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "5": [
+                    [
+                        "SAVANA_CLASSIFY",
+                        "savana",
+                        "1.3.7"
+                    ]
+                ],
+                "classified_vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.classified.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "germline_vcf": [
+
+                ],
+                "legacy_vcfs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.classified.lenient.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.classified.strict.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "somatic_bedpe": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.classified.somatic.bedpe:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "somatic_vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.classified.somatic.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_savana": [
+                    [
+                        "SAVANA_CLASSIFY",
+                        "savana",
+                        "1.3.7"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-21T13:57:00.059950477",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}