New module: clusty

modules/nf-core/clusty/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::clusty=1.2.2"

modules/nf-core/clusty/main.nf

@@ -0,0 +1,50 @@
+
+process CLUSTY {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/clusty:1.2.2--h9ee0642_0':
+        'biocontainers/clusty:1.2.2--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(distances)
+    tuple val(meta2), path(objects)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: assignments
+    tuple val("${task.process}"), val('clusty'), eval('echo $(clusty --version 2>&1)'), topic: versions, emit: versions_clusty
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def objects_arg = objects ? "--objects-file $objects" : ""
+
+    if ("${distances}" == "${prefix}.tsv") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    clusty \\
+        $args \\
+        -t $task.cpus \\
+        ${objects_arg} \\
+        ${distances} \\
+        ${prefix}.tsv
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def objects_arg = objects ? "--objects-file $objects" : ""
+
+    if ("${distances}" == "${prefix}.tsv") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    echo $args
+    echo ${objects_arg}
+    touch ${prefix}.tsv
+    """
+}

modules/nf-core/clusty/meta.yml

@@ -0,0 +1,83 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "clusty"
+description: Clusty is a tool for large-scale clustering using sparse distance
+  matrices, suitable for datasets with millions of objects.
+keywords:
+  - cluster
+  - network
+  - contig
+  - scaffold
+  - alignment
+  - protein
+tools:
+  - "clusty":
+      description: "Clusty is a tool for large-scale data clustering."
+      homepage: "https://github.com/refresh-bio/clusty"
+      documentation: "https://github.com/refresh-bio/clusty"
+      tool_dev_url: "https://github.com/refresh-bio/clusty"
+      doi: "10.1038/s41592-025-02701-7"
+      licence: ["GPL v3-or-later"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - distances:
+        type: file
+        description: pairwise distances file (e.g., TSV format)
+        pattern: "*.tsv"
+        ontologies:
+          - edam: "http://edamontology.org/format_3475" # TSV
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - objects:
+        type: file
+        description: Optional TSV file containing object identifiers
+        pattern: "*.tsv"
+        ontologies:
+          - edam: "http://edamontology.org/format_3475" # TSV
+
+output:
+  assignments:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.tsv":
+          type: file
+          description: TSV file with cluster assignments
+          pattern: "*.tsv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475" # TSV
+  versions_clusty:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - clusty:
+          type: string
+          description: The name of the tool
+      - "echo $(clusty --version 2>&1":
+          type: string
+          description: The version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - clusty:
+          type: string
+          description: The name of the tool
+      - "echo $(clusty --version 2>&1":
+          type: string
+          description: The version of the tool
+authors:
+  - "@Joon-Klaps"
+maintainers:
+  - "@Joon-Klaps"

modules/nf-core/clusty/tests/main.nf.test

@@ -0,0 +1,92 @@
+nextflow_process {
+    name "Test Process CLUSTY"
+    script "../main.nf"
+    process "CLUSTY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "clusty"
+
+    test("generic - only distances") {
+
+        when {
+            params {
+                clusty_args = '--id-cols id1 id2 --distance-col ani --similarity --min ani 0.70'
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'generic/tsv/ani.tsv', checkIfExists: true),
+                ]
+                input[1] = [[:], []]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("generic - distances - objects") {
+
+        when {
+            params {
+                clusty_args = '--id-cols name1 name2 --distance-col ani --similarity --min ani 0.70'
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'generic/tsv/ani.tsv', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'generic/txt/ani_ids.txt', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("generic - only distances - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                clusty_args = '--id-cols name1 name2 --distance-col ani --similarity --min ani 0.70'
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'generic/tsv/ani.tsv', checkIfExists: true),
+                ]
+                input[1] = [[:], []]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/clusty/tests/main.nf.test.snap

@@ -0,0 +1,125 @@
+{
+    "generic - distances - objects": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,cea71211069e4aeed9e021ebebc038e7"
+                    ]
+                ],
+                "1": [
+                    [
+                        "CLUSTY",
+                        "clusty",
+                        "1.2.2"
+                    ]
+                ],
+                "assignments": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,cea71211069e4aeed9e021ebebc038e7"
+                    ]
+                ],
+                "versions_clusty": [
+                    [
+                        "CLUSTY",
+                        "clusty",
+                        "1.2.2"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-09T12:35:44.503401"
+    },
+    "generic - only distances - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "CLUSTY",
+                        "clusty",
+                        "1.2.2"
+                    ]
+                ],
+                "assignments": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_clusty": [
+                    [
+                        "CLUSTY",
+                        "clusty",
+                        "1.2.2"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-09T12:36:00.849772"
+    },
+    "generic - only distances": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,9c4d0da996fe7c4579b473f4148623ec"
+                    ]
+                ],
+                "1": [
+                    [
+                        "CLUSTY",
+                        "clusty",
+                        "1.2.2"
+                    ]
+                ],
+                "assignments": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,9c4d0da996fe7c4579b473f4148623ec"
+                    ]
+                ],
+                "versions_clusty": [
+                    [
+                        "CLUSTY",
+                        "clusty",
+                        "1.2.2"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-09T12:35:28.037382"
+    }
+}

modules/nf-core/clusty/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: CLUSTY {
+        ext.args = params.clusty_args
+    }
+}