New module: GRIMER

modules/nf-core/grimer/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::grimer=1.1.0"

modules/nf-core/grimer/main.nf

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+process GRIMER {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/grimer:1.1.0--pyhdfd78af_0':
+        'quay.io/biocontainers/grimer:1.1.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(input_table)
+    path sample_metadata
+    path config
+
+    output:
+    tuple val(meta), path("*.html"), emit: report
+    tuple val("${task.process}"), val('grimer'), eval('grimer --version 2>&1 | tail -1'), emit: versions_grimer, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def m_arg  = sample_metadata ? "-m ${sample_metadata}" : ''
+    def c_arg  = config          ? "-c ${config}"   : ''
+    """
+    grimer \\
+        -i ${input_table} \\
+        ${m_arg} \\
+        ${c_arg} \\
+        -o ${prefix}.html \\
+        ${args}
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+    """
+}

modules/nf-core/grimer/meta.yml

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+name: grimer
+description: |
+  Generates an interactive HTML dashboard integrating taxonomy,
+  annotation, and metadata to detect contamination in metagenomic
+  and amplicon sequencing datasets. GRIMER is independent of
+  quantification methods and directly analyses contingency tables.
+keywords:
+  - metagenomics
+  - contamination
+  - visualisation
+  - taxonomy
+  - viromics
+  - microbiome
+  - dashboard
+tools:
+  - grimer:
+      description: |
+        GRIMER performs automated contamination analysis and generates
+        portable interactive dashboards from contingency tables,
+        integrating taxonomy, annotation and metadata.
+      homepage: https://github.com/pirovc/grimer
+      documentation: https://pirovc.github.io/grimer/
+      tool_dev_url: https://github.com/pirovc/grimer
+      doi: "10.1101/2021.06.22.449360"
+      licence:
+        - "MIT"
+      identifier: biotools:grimer
+      args_id: "$args"
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. [ id:'sample1' ]
+    - input_table:
+        type: file
+        description: |
+          Tab-separated count/observation table or .biom file.
+          Rows are observations; columns are samples.
+        pattern: "*.{tsv,biom}"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+          - edam: http://edamontology.org/format_3746
+  - sample_metadata:
+      type: file
+      description: Tab-separated metadata file. Rows are samples; columns are
+        metadata fields. Optional, pass [] to omit.
+      pattern: "*.tsv"
+      ontologies:
+        - edam: http://edamontology.org/format_3475
+  - config:
+      type: file
+      description: |
+        YAML configuration file defining external tool references,
+        controls, and annotations. Optional, pass [] to omit.
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750
+output:
+  report:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information.
+      - "*.html":
+          type: file
+          description: |
+            Interactive HTML dashboard report integrating taxonomy,
+            contamination analysis, heatmaps, and correlation plots.
+          pattern: "*.html"
+          ontologies: []
+  versions_grimer:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - grimer:
+          type: string
+          description: The name of the tool
+      - grimer --version 2>&1 | tail -1:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - grimer:
+          type: string
+          description: The name of the tool
+      - grimer --version 2>&1 | tail -1:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@Jonahnki"
+maintainers:
+  - "@Jonahnki"

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

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+nextflow_process {
+
+    name "Test Process GRIMER"
+    script "../main.nf"
+    process "GRIMER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "grimer"
+
+    test("grimer - tsv - basic") {
+
+        when {
+            process {
+                """
+                def count_table = file(workDir.resolve("test_count_table.tsv").toString())
+                count_table.text = [
+                    "#OTU_ID\tsample1\tsample2\tsample3",
+                    "Bacteria;Proteobacteria\t1250\t890\t2100",
+                    "Bacteria;Firmicutes\t430\t1200\t320",
+                    "Viruses;Caudoviricetes\t45\t120\t88"
+                ].join("\\n") + "\\n"
+
+                input[0] = [
+                    [ id:"test_sample" ],
+                    count_table
+                ]
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("grimer - tsv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                def count_table = file(workDir.resolve("test_count_table.tsv").toString())
+                count_table.text = [
+                    "#OTU_ID\tsample1\tsample2\tsample3",
+                    "Bacteria;Proteobacteria\t1250\t890\t2100",
+                    "Bacteria;Firmicutes\t430\t1200\t320",
+                    "Viruses;Caudoviricetes\t45\t120\t88"
+                ].join("\\n") + "\\n"
+
+                input[0] = [
+                    [ id:"test_stub" ],
+                    count_table
+                ]
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

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

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+{
+    "grimer - tsv - basic": {
+        "content": [
+            {
+                "versions_grimer": [
+                    [
+                        "GRIMER",
+                        "grimer",
+                        "1.1.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-26T00:00:00.000000000",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    },
+    "grimer - tsv - stub": {
+        "content": [
+            {
+                "versions_grimer": [
+                    [
+                        "GRIMER",
+                        "grimer",
+                        "1.1.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-26T00:00:00.000000000",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    }
+}