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JonahnkiSPPearce
Jonahnki
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SPPearce
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New module: GRIMER (#11663)
* Add GRIMER module for interactive metagenome contamination visualisation * fix: use existing test-datasets file for stub test * fix: restore meta2/meta3 input descriptions, rename optional inputs, add stub snapshot, revert .nf-core.yml * fix(grimer): address reviewer comments - rename optional inputs, fix meta.yml, update tests * fix(grimer): fix version capture to strip ASCII banner * fix: resolve multi-line string interpolation issues in grimer test stub * fix: use workDir.resolve for on-the-fly test file creation * fix(grimer): fix version eval and regenerate snapshot * fix(grimer): fix version eval to strip ASCII banner, update meta.yml and snapshot * fix: add versions to placeholder snapshot to satisfy lint * fix: apply SPPearce suggested assertion pattern - snapshot filename and versions only * test: regenerate snapshot with real GRIMER output * fix: strip grimer prefix from version string in eval * fix: strip grimer prefix from version string, update snapshot, sync meta.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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‎modules/nf-core/grimer/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- "bioconda::grimer=1.1.0"

‎modules/nf-core/grimer/main.nf‎

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

‎modules/nf-core/grimer/meta.yml‎

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

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

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

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

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{
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"grimer - tsv - basic": {
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"content": [
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"test_sample.html",
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{
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"versions_grimer": [
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[
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"GRIMER",
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"grimer",
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"1.1.0"
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]
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]
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}
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],
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"timestamp": "2026-06-04T13:24:01.89404156",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.04.6"
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}
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},
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"grimer - tsv - stub": {
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"content": [
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"test_stub.html",
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{
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"versions_grimer": [
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[
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"GRIMER",
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"grimer",
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"1.1.0"
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]
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]
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}
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],
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"timestamp": "2026-06-04T13:25:24.167541988",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.04.6"
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}
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}
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}

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