New module: exomiser/analyse

modules/nf-core/exomiser/analyse/main.nf

@@ -0,0 +1,68 @@
+process EXOMISER_ANALYSE {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    container "nf-core/exomiser-cli:15.0.0-bash"
+
+    input:
+    tuple val(meta), path(vcf), path(ped), val(assembly), path(phenopacket), path(analysis_script)
+    tuple val(meta2), path(reference_cache, stageAs: 'exomiser_data/*'), val(reference_version)
+    tuple val(meta3), path(phenotype_cache, stageAs: 'exomiser_data/*'), val(phenotype_version)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    tuple val(meta), path("*.json"), emit: json
+    tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), path("*.parquet"), emit: parquet
+    tuple val(meta), path("*.vcf"), emit: vcf
+    tuple val("${task.process}"), val('exomiser'), eval("exomiser --version"), topic: versions, emit: versions_exomiser
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("EXOMISER_ANALYSE module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def ped_cmd = ped ? "--ped=${ped}" : ""
+    def phenopacket_cmd = phenopacket ? "--sample=${phenopacket}" : ""
+    def assembly_cmd = assembly ? "--assembly=${assembly}" : ""
+    def analysis_cmd = analysis_script ? "--analysis ${analysis_script}" : ""
+    def vcf_cmd = vcf ? "--vcf=${vcf}" : ""
+
+    """
+        export EXOMISER_DATA_DIRECTORY=./exomiser_data
+        export EXOMISER_${assembly}_DATA_VERSION=${reference_version}
+        export EXOMISER_PHENOTYPE_DATA_VERSION=${phenotype_version}
+
+        exomiser analyse \\
+        ${ped_cmd} \\
+        ${phenopacket_cmd} \\
+        ${assembly_cmd} \\
+        ${vcf_cmd}\\
+        ${analysis_cmd} \\
+        ${args} \\
+        --output-directory=\$PWD \\
+        --output-filename=${prefix}
+    """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("EXOMISER_ANALYSE module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo ${args}
+    touch ${prefix}.tsv
+    touch ${prefix}.json
+    touch ${prefix}.html
+    touch ${prefix}.parquet
+    touch ${prefix}.vcf
+    """
+}

modules/nf-core/exomiser/analyse/meta.yml

@@ -0,0 +1,153 @@
+name: "exomiser_analyse"
+description: Phenotype-driven variant prioritisation for rare Mendelian
+  disorders.
+keywords:
+  - exomiser
+  - variant prioritisation
+  - rare disease
+  - Mendelian disorders
+tools:
+  - "exomiser":
+      description: "A Tool to Annotate and Prioritize Exome Variants"
+      homepage: "https://exomiser.readthedocs.io/en/stable/"
+      documentation: "https://exomiser.readthedocs.io/en/stable/"
+      tool_dev_url: "https://github.com/exomiser/Exomiser"
+      doi: "10.1038/s41525-024-00456-2"
+      licence:
+        - "AGPL-3.0"
+      identifier: biotools:exomiser
+input:
+  - - meta:
+        type: map
+        description: Groovy Map containing sample information. e.g. `[
+          id:'sample1' ]`
+    - vcf:
+        type: file
+        description: "VCF file containing variants to be analysed."
+        pattern: "*.vcf.gz"
+        ontologies:
+          - edam: http://edamontology.org/format_3989
+    - ped:
+        type: file
+        description: "PED file containing family information."
+        pattern: "*.ped"
+        ontologies: []
+    - assembly:
+        type: string
+        description: "Genome assembly to use. e.g. GRCh37, GRCh38"
+    - phenopacket:
+        type: file
+        description: "Phenopacket file containing phenotype information."
+        pattern: "*.{yml,yaml,json}"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+          - edam: http://edamontology.org/format_3464
+    - analysis_script:
+        type: file
+        description: "Custom analysis script for Exomiser analysis"
+        pattern: "*.{yml,yaml,json}"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+          - edam: http://edamontology.org/format_3464
+  - - meta2:
+        type: map
+        description: Groovy Map containing reference cache information. e.g. `[
+          id:'sample1' ]`
+    - reference_cache:
+        type: file
+        description: "Reference cache for Exomiser analysis"
+        pattern: "exomiser_data/*"
+        ontologies: []
+    - reference_version:
+        type: string
+        description: "Reference version for Exomiser analysis"
+  - - meta3:
+        type: map
+        description: Groovy Map containing phenotype cache information. e.g. `[
+          id:'sample1' ]`
+    - phenotype_cache:
+        type: file
+        description: "Phenotype cache for Exomiser analysis"
+        pattern: "exomiser_data/*"
+        ontologies: []
+    - phenotype_version:
+        type: string
+        description: "Phenotype version for Exomiser analysis"
+output:
+  tsv:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[
+            id:'sample1' ]`
+      - "*.tsv":
+          type: file
+          description: "TSV file containing prioritized variants."
+          pattern: "*.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475
+  json:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[
+            id:'sample1' ]`
+      - "*.json":
+          type: file
+          description: "JSON file containing prioritized variants."
+          pattern: "*.json"
+          ontologies:
+            - edam: http://edamontology.org/format_3464
+  html:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[
+            id:'sample1' ]`
+      - "*.html":
+          type: file
+          description: "HTML file containing prioritized variants."
+          pattern: "*.html"
+          ontologies: []
+  parquet:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[
+            id:'sample1' ]`
+      - "*.parquet":
+          type: file
+          description: "Parquet file containing prioritized variants."
+          pattern: "*.parquet"
+          ontologies: []
+  vcf:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[
+            id:'sample1' ]`
+      - "*.vcf":
+          type: file
+          description: "VCF file containing prioritized variants."
+          pattern: "*.vcf"
+          ontologies: []
+  versions_exomiser:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - exomiser:
+          type: string
+          description: The name of the tool
+      - exomiser --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
+      - exomiser:
+          type: string
+          description: The name of the tool
+      - exomiser --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@matthdsm"
+maintainers:
+  - "@matthdsm"

modules/nf-core/exomiser/analyse/tests/main.nf.test

@@ -0,0 +1,48 @@
+nextflow_process {
+
+    name "Test Process EXOMISER_ANALYSE"
+    script "../main.nf"
+    process "EXOMISER_ANALYSE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "exomiser"
+    tag "exomiser/analyse"
+
+    test("homo_sapiens - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.vcf.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/ped/test.ped'),
+                    "GRCh38",
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/phenopacket/test.yml'),
+                    []
+                ]
+                input[1] = [
+                    [ id:'test' ],
+                    file("s3://nf-core-reference-data/exomiser/GRCh38/1234/reference_cache"),
+                    "1234"
+                ]
+                input[2] = [
+                    [ id:'test' ],
+                    file("s3://nf-core-reference-data/exomiser/GRCh38/1234/phenotype_cache"),
+                    "1234"
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
+            )
+        }
+    }
+}

modules/nf-core/exomiser/analyse/tests/main.nf.test.snap

@@ -0,0 +1,16 @@
+{
+    "homo_sapiens - vcf - stub": {
+        "content": [
+            {
+                "versions_exomiser": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-03-23T19:09:41.158068"
+    }
+}