bots add new module for svdss/index

modules/nf-core/svdss/index/environment.yml

@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/svdss
+  - bioconda::svdss=2.1.1

modules/nf-core/svdss/index/main.nf

@@ -0,0 +1,43 @@
+process SVDSS_INDEX {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/svdss:2.1.1--he17396a_0' :
+        'quay.io/biocontainers/svdss:2.1.1--he17396a_0' }"
+
+    input:
+    tuple val(meta), path(fasta), path(existing_index)
+    val output_format
+
+    output:
+    tuple val(meta), path("${prefix}.${output_format}"), emit: index
+    tuple val("${task.process}"), val('svdss'), eval("SVDSS --version 2>&1 | sed 's/SVDSS, v//'"), emit: versions_svdss, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def format_flag = output_format == 'fmd' ? '-d' : '-b'
+    def existing_index_arg = existing_index ? "-i ${existing_index}" : ''
+    """
+    SVDSS index \\
+        -t ${task.cpus} \\
+        ${existing_index_arg} \\
+        ${format_flag} ${fasta} \\
+        ${args} \\
+        > ${prefix}.${output_format}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+
+    touch ${prefix}.${output_format}
+    """
+}

modules/nf-core/svdss/index/meta.yml

@@ -0,0 +1,82 @@
+name: svdss_index
+description: Index a reference genome FASTA file using SVDSS (via ropebwt3), producing either an FMD or FMR index for use with SVDSS smooth and search subcommands
+keywords:
+  - structural variants
+  - sv calling
+  - indexing
+  - reference genome
+  - fm-index
+tools:
+  - svdss:
+      description: |
+        SVDSS is a tool for structural variant discovery from short-read sequencing data.
+        It implements an FM-index-based approach to efficiently detect SVs against a reference genome.
+      homepage: https://github.com/Parsoa/SVDSS
+      documentation: https://github.com/Parsoa/SVDSS
+      tool_dev_url: https://github.com/Parsoa/SVDSS
+      doi: "10.1038/s41592-022-01674-1"
+      licence:
+        - "MIT"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: Reference genome in FASTA format
+        pattern: "*.{fasta,fa,fna}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
+    - existing_index:
+        type: file
+        description: |
+          Optional path to an existing index file to read and extend (passed via -i).
+          Set to [] when not used.
+        pattern: "*.{fmd,fmr}"
+        ontologies: []
+  - output_format:
+      type: string
+      description: |
+        Output index format. Use 'fmd' for the fermi-delta format (adds -d flag)
+        or 'fmr' for the ropebwt format (adds -b flag).
+      pattern: "fmd|fmr"
+output:
+  index:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}.${output_format}:
+          type: file
+          description: FM-index file produced by SVDSS index, used as input for SVDSS smooth and search
+          pattern: "*.{fmd,fmr}"
+          ontologies: []
+  versions_svdss:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - svdss:
+          type: string
+          description: The name of the tool
+      - SVDSS --version 2>&1 | sed 's/SVDSS, v//':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - svdss:
+          type: string
+          description: The name of the tool
+      - SVDSS --version 2>&1 | sed 's/SVDSS, v//':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@vagkaratzas"
+maintainers:
+  - "@vagkaratzas"

modules/nf-core/svdss/index/tests/main.nf.test

@@ -0,0 +1,86 @@
+nextflow_process {
+
+    name "Test Process SVDSS_INDEX"
+    script "../main.nf"
+    process "SVDSS_INDEX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "svdss"
+    tag "svdss/index"
+
+    test("sarscov2 - genome fasta - fmd") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    []
+                ]
+                input[1] = 'fmd'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - genome fasta - fmr") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    []
+                ]
+                input[1] = 'fmr'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - genome fasta - fmd - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    []
+                ]
+                input[1] = 'fmd'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/svdss/index/tests/main.nf.test.snap

@@ -0,0 +1,80 @@
+{
+    "sarscov2 - genome fasta - fmd - stub": {
+        "content": [
+            {
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fmd:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_svdss": [
+                    [
+                        "SVDSS_INDEX",
+                        "svdss",
+                        "2.1.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-04-23T19:29:18.443950745"
+    },
+    "sarscov2 - genome fasta - fmd": {
+        "content": [
+            {
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fmd:md5,e07e753be2f2b6e6354963a1b44a0256"
+                    ]
+                ],
+                "versions_svdss": [
+                    [
+                        "SVDSS_INDEX",
+                        "svdss",
+                        "2.1.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-04-23T19:29:07.682526462"
+    },
+    "sarscov2 - genome fasta - fmr": {
+        "content": [
+            {
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fmr:md5,45ecc6cf667105098c01cc32ec255561"
+                    ]
+                ],
+                "versions_svdss": [
+                    [
+                        "SVDSS_INDEX",
+                        "svdss",
+                        "2.1.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-04-23T19:29:12.935284928"
+    }
+}