Add poppunk/createdb module

modules/nf-core/poppunk/createdb/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::poppunk=2.7.8"

modules/nf-core/poppunk/createdb/main.nf

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+process POPPUNK_CREATEDB {
+    tag "$meta.id"
+    label 'process_medium'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/poppunk:2.7.8--py310h4d0eb5b_0' :
+        'biocontainers/poppunk:2.7.8--py310h4d0eb5b_0' }"
+    input:
+    tuple val(meta), path(r_file), path(fasta)
+    output:
+    tuple val(meta), path("${meta.id}"),                    emit: db
+    tuple val(meta), path("${meta.id}/${meta.id}.h5"),      emit: h5
+    tuple val(meta), path("${meta.id}/${meta.id}.dists.*"), emit: dists
+    tuple val("${task.process}"), val('poppunk'), eval("poppunk --version 2>&1 | head -1 | sed 's/^.*v//'"), topic: versions, emit: versions_poppunk
+    when:
+    task.ext.when == null || task.ext.when
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    poppunk \\
+        --create-db \\
+        --r-files ${r_file} \\
+        --output ${prefix} \\
+        --threads ${task.cpus} \\
+        --qc-keep \\
+        ${args}
+    """
+    stub:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}
+    touch ${prefix}/${prefix}.h5
+    touch ${prefix}/${prefix}.dists.pkl
+    touch ${prefix}/${prefix}.dists.npy
+    touch ${prefix}/${prefix}.refs
+    touch ${prefix}/qcreport.txt
+    """
+}

modules/nf-core/poppunk/createdb/meta.yml

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+name: "poppunk_createdb"
+description: Create a PopPUNK database of kmer sketches and pairwise distances
+  from a set of assemblies
+keywords:
+  - genomics
+  - bacteria
+  - clustering
+  - sketching
+  - poppunk
+tools:
+  - "poppunk":
+      description: "PopPUNK (POPulation Partitioning Using Nucleotide Kmers) - rapid
+        bacterial population analysis. Note: this module runs with --qc-filter continue
+        by default; override via task.ext.args."
+      homepage: "https://poppunk.bacpop.org/index.html"
+      documentation: "https://poppunk.bacpop.org/index.html"
+      tool_dev_url: "https://github.com/bacpop/PopPUNK"
+      doi: "10.1101/gr.241455.118"
+      licence:
+        - "Apache-2.0"
+      identifier: biotools:poppunk
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - r_file:
+        type: file
+        description: |
+          Tab-separated file listing sample names and paths to their assembly FASTA files.
+          Format: <sample_name>\t<path/to/assembly.fa>
+        pattern: "*.{txt,tsv}"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+    - fasta:
+        type: file
+        description: List of assembly FASTA files for all samples listed in the
+          r_file
+        pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929
+output:
+  db:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${meta.id}:
+          type: directory
+          description: Directory containing the full PopPUNK database output files
+  h5:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${meta.id}/${meta.id}.h5:
+          type: file
+          description: HDF5 file containing the k-mer sketches for all input
+            genomes
+          pattern: "*.h5"
+          ontologies: []
+  dists:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${meta.id}/${meta.id}.dists.*:
+          type: file
+          description: Pairwise distance matrix files (numpy and pickle format)
+          pattern: "*.dists.*"
+          ontologies: []
+  versions_poppunk:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - poppunk:
+          type: string
+          description: The name of the tool
+      - poppunk --version 2>&1 | head -1 | sed 's/^.*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
+      - poppunk:
+          type: string
+          description: The name of the tool
+      - poppunk --version 2>&1 | head -1 | sed 's/^.*v//':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@cwoodside1278"
+maintainers:
+  - "@cwoodside1278"

modules/nf-core/poppunk/createdb/tests/main.nf.test

@@ -0,0 +1,41 @@
+nextflow_process {
+    name "Test Process POPPUNK_CREATEDB"
+    script "../main.nf"
+    process "POPPUNK_CREATEDB"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "poppunk"
+    tag "poppunk/createdb"
+
+    // PopPUNK requires a minimum number of sufficiently diverse same-species genomes
+    // to compute meaningful k-mer distances. No suitable tiny test data exists in
+    // nf-core/test-datasets, so only a stub test is provided here.
+    // To test with real data, run manually with multiple same-species genome FASTAs,
+    // e.g. multiple H. influenzae strains from NCBI.
+
+    test("haemophilus_influenzae - fasta - createdb - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                def fasta1 = file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true)
+                def fasta2 = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/fasta/haemophilus_influenzae.fna.gz', checkIfExists: true)
+                def rfile = file(workDir.toString() + '/rfile.txt')
+                rfile.text = ["sample1", "genome.fna.gz"].join("\t") + System.lineSeparator() +
+                             ["sample2", "haemophilus_influenzae.fna.gz"].join("\t") + System.lineSeparator()
+                input[0] = [
+                    [ id:'test' ],
+                    rfile,
+                    [fasta1, fasta2]
+                ]
+                """
+            }
+        }
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/poppunk/createdb/tests/main.nf.test.snap

@@ -0,0 +1,93 @@
+{
+    "haemophilus_influenzae - fasta - createdb - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "qcreport.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.dists.npy:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.dists.pkl:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.h5:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.refs:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.h5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.dists.npy:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.dists.pkl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "3": [
+                    [
+                        "POPPUNK_CREATEDB",
+                        "poppunk",
+                        "poppunk 2.7.8"
+                    ]
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "qcreport.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.dists.npy:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.dists.pkl:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.h5:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.refs:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "dists": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.dists.npy:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.dists.pkl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "h5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.h5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_poppunk": [
+                    [
+                        "POPPUNK_CREATEDB",
+                        "poppunk",
+                        "poppunk 2.7.8"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-02T19:53:41.29162914",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    }
+}