WIP: new module: MultiQC_SAV

modules/nf-core/multiqc_sav/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::multiqc=1.33
+  - bioconda::multiqc_sav=0.2.1

modules/nf-core/multiqc_sav/main.nf

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+process MULTIQC_SAV {
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' :
+        'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b' }"
+
+    input:
+    tuple val(meta), path(runinfo_xml), path(interop_bin, stageAs: "InterOp/*")
+    path(extra_multiqc_files, stageAs: "?/*")
+    path(multiqc_config)
+    path(extra_multiqc_config)
+    path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
+
+    output:
+    path "*.html"      , emit: report
+    path "*_data"      , emit: data
+    path "*_plots"     , optional:true, emit: plots
+    tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), val('multiqc_sav'), eval('python -c "import multiqc_sav; print(multiqc_sav.__version__)"'), emit: versions
+    // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
+    def config = multiqc_config ? "--config ${multiqc_config}" : ''
+    def extra_config = extra_multiqc_config ? "--config ${extra_multiqc_config}" : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
+    """
+    multiqc \\
+        --force \\
+        ${args} \\
+        ${config} \\
+        ${prefix} \\
+        ${extra_config} \\
+        ${logo} \\
+        ${replace} \\
+        ${samples} \\
+        .
+    """
+
+    stub:
+    """
+    mkdir multiqc_data
+    touch multiqc_data/.stub
+    mkdir multiqc_plots
+    touch multiqc_report.html
+    """
+}

modules/nf-core/multiqc_sav/meta.yml

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+name: multiqc_sav
+description: Aggregate results from bioinformatics analyses across many samples into a single report, with support for multiqc_sav plugin
+keywords:
+  - QC
+  - bioinformatics tools
+  - Beautiful stand-alone HTML report
+  - Illumina
+  - Sequencing Analysis Viewer
+  - SAV
+tools:
+  - multiqc:
+      description: |
+        MultiQC searches a given directory for analysis logs and compiles a HTML report.
+        It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+      homepage: https://multiqc.info/
+      documentation: https://multiqc.info/docs/
+      licence: ["GPL-3.0-or-later"]
+      identifier: biotools:multiqc
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'sample1', single_end:false ]
+    - runinfo_xml:
+        type: file
+        description: Illumina RunInfo.xml file
+        pattern: "RunInfo.xml"
+        ontologies: [http://edamontology.org/format_2332] # XML format
+    - interop_bin:
+        type: file
+        description: Illumina InterOp binary files
+        pattern: "InterOp/*.bin"
+        ontologies: [http://edamontology.org/format_2333] # Binary format
+  - extra_multiqc_files:
+      type: file
+      description: |
+        List of reports / files rec ognised by MultiQC, for example the html and zip output of FastQC
+      ontologies: []
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections
+        in multiqc_config.
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+      ontologies: []
+  - replace_names:
+      type: file
+      description: |
+        Optional two-column sample renaming file. First column a set of
+        patterns, second column a set of corresponding replacements. Passed via
+        MultiQC's `--replace-names` option.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+  - sample_names:
+      type: file
+      description: |
+        Optional TSV file with headers, passed to the MultiQC --sample_names
+        argument.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+output:
+  report:
+    - "*.html":
+        type: file
+        description: MultiQC report file
+        pattern: ".html"
+        ontologies: []
+  data:
+    - "*_data":
+        type: directory
+        description: MultiQC data dir
+        pattern: "multiqc_data"
+  plots:
+    - "*_plots":
+        type: file
+        description: Plots created by MultiQC
+        pattern: "*_data"
+        ontologies: []
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - multiqc:
+          type: string
+          description: The tool name
+      - multiqc --version | sed "s/.* //g":
+          type: eval
+          description: The expression to obtain the version of the tool
+      - multiqc_sav:
+          type: string
+          description: The tool name
+      - python -c "import multiqc_sav; print(multiqc_sav.__version__)":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@matthdsm"
+maintainers:
+  - "@matthdsm"

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

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+nextflow_process {
+
+    name "Test Process MULTIQC_SAV"
+    script "../main.nf"
+    process "MULTIQC_SAV"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "multiqc_sav"
+
+    config "./nextflow.config"
+
+    test("NovaSeq6000") {
+        setup {
+            run("UNTAR") {
+                script "../../untar/main.nf"
+                process {
+                """
+                input[0] = [[ id: 'NovaSeq6000' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bcl/200624_A00834_0183_BHMTFYDRXX.tar.gz', checkIfExists: true)]
+                """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                ch_sav_in = UNTAR.out.untar.map{ meta, untar -> 
+                    def xml = untar.eachFileRecurse { file -> 
+                        if (file.name == 'RunInfo.xml') {
+                            return file
+                        }
+                    }.findAll{ it != null }[0]
+
+                    def interop = []
+                    untar.eachFileRecurse { file -> 
+                        if (file.parentFile.name == 'InterOp') {
+                            interop << file
+                        }
+                    }
+                    return [meta, xml, interop]
+                }
+
+                input[0] = ch_sav_in
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }
+            )
+        }
+
+    }
+}

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

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+{
+    "sarscov2 single-end [fastqc]": {
+        "content": [
+            {
+                "versions": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.33"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-09T10:10:43.020315838"
+    },
+    "sarscov2 single-end [fastqc] - stub": {
+        "content": [
+            [
+                "multiqc_report.html",
+                "multiqc_data",
+                "multiqc_plots",
+                {
+                    "versions": [
+                        [
+                            "MULTIQC",
+                            "multiqc",
+                            "1.33"
+                        ]
+                    ]
+                }
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-09T10:11:14.131950776"
+    },
+    "sarscov2 single-end [fastqc] [config]": {
+        "content": [
+            {
+                "versions": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.33"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-09T10:11:07.15692209"
+    }
+}

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

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+process {
+    withName: 'MULTIQC_SAV' {
+        ext.prefix = null
+    }
+}