added pcne module

modules/nf-core/pcne/environment.yml

@@ -0,0 +1,6 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::pcne=3.3.1"

modules/nf-core/pcne/main.nf

@@ -0,0 +1,49 @@
+process PCNE {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/pcne%3A3.3.1--hdfd78af_0'
+        : 'quay.io/biocontainers/pcne:3.3.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    tuple val(meta2), path(chromosome)
+    tuple val(meta3), path(plasmids)
+
+    output:
+    tuple val(meta), path("*_results.tsv"), emit: results
+    tuple val(meta), path("*.log"), emit: log
+    tuple val(meta), path("*.png"), emit: plots, optional: true
+    tuple val("${task.process}"), val('pcne'), eval("pcne -v | grep 'version' | tail -n 1 | sed 's/.*version //'"), topic: versions, emit: versions_pcne
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def is_bam = reads.toString().endsWith('.bam')
+    def input_cmd = is_bam ? "-b ${reads}" : "-r ${reads[0]} -R ${reads[1]}"
+
+    def plasmid_cmd = plasmids instanceof List ? plasmids.join(' ') : plasmids
+
+    """
+    pcne \\
+        -c ${chromosome} \\
+        -p ${plasmid_cmd} \\
+        ${input_cmd} \\
+        -o ${prefix} \\
+        -t ${task.cpus} \\
+        ${args}
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_results.tsv
+    touch ${prefix}.log
+    """
+}

modules/nf-core/pcne/meta.yml

@@ -0,0 +1,110 @@
+name: "pcne"
+description: "Estimates plasmid copy number from assembled genome"
+keywords:
+  - plasmid
+  - copy number
+  - genomics
+  - alignment
+  - coverage
+tools:
+  - "pcne":
+      description: "Estimates plasmid copy number from assembled genome."
+      homepage: "https://github.com/riccabolla/PCNE"
+      documentation: "https://github.com/riccabolla/PCNE"
+      tool_dev_url: "https://github.com/riccabolla/PCNE"
+      doi: "10.1177/11779322251410037"
+      licence:
+        - "MIT"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - reads:
+        type: file
+        description: FASTQ reads (paired or single) or a pre-aligned BAM file
+        pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1930"
+          - edam: "http://edamontology.org/format_2572"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference chromosome information
+          e.g. `[ id:'genome' ]`
+    - chromosome:
+        type: file
+        description: Chromosome contigs FASTA file
+        pattern: "*.{fasta,fa,fasta.gz,fa.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference plasmid information
+          e.g. `[ id:'plasmids' ]`
+    - plasmids:
+        type: file
+        description: One or more plasmid FASTA files
+        pattern: "*.{fasta,fa,fasta.gz,fa.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+output:
+  results:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*_results.tsv":
+          type: file
+          description: TSV file containing the estimated plasmid copy numbers
+          pattern: "*_results.tsv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475"
+  log:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.log":
+          type: file
+          description: PCNE run log file
+          pattern: "*.log"
+          ontologies:
+            - edam: "http://edamontology.org/format_2330"
+  plots:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.png":
+          type: file
+          description: Bar plot of plasmid copy numbers or GC vs Depth diagnostic
+            plots
+          pattern: "*.png"
+          ontologies:
+            - edam: "http://edamontology.org/format_3603"
+  versions_pcne:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "pcne":
+          type: string
+          description: The name of the tool
+      - "pcne -v | grep 'version' | tail -n 1 | sed 's/.*version //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "pcne":
+          type: string
+          description: The name of the tool
+      - "pcne -v | grep 'version' | tail -n 1 | sed 's/.*version //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@riccabolla"
+maintainers:
+  - "@riccabolla"

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

@@ -0,0 +1,69 @@
+nextflow_process {
+
+    name "Test Process PCNE"
+    script "../main.nf"
+    process "PCNE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pcne"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id: 'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id: 'transcriptome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(sanitizeOutput(process.out)).match()
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id: 'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id: 'transcriptome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(sanitizeOutput(process.out)).match()
+        }
+
+    }
+
+}

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

@@ -0,0 +1,80 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "plots": [
+
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_pcne": [
+                    [
+                        "PCNE",
+                        "pcne",
+                        "3.3.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-29T17:10:13.997705663",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 - bam": {
+        "content": [
+            {
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,9b282212a32df78088bdcb7a173df4ce"
+                    ]
+                ],
+                "plots": [
+
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_results.tsv:md5,2efc4a2d2c671eeda63ce2a4aeb81fc6"
+                    ]
+                ],
+                "versions_pcne": [
+                    [
+                        "PCNE",
+                        "pcne",
+                        "3.3.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-29T17:09:56.768899583",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}