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New module ngsbits/rohhunter (#12005)
new module ngsbits/rohhunter
1 parent a40ca37 commit fd91924

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‎modules/nf-core/ngsbits/rohhunter/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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# renovate: datasource=conda depName=bioconda/ngs-bits
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- bioconda::ngs-bits=2025_09

‎modules/nf-core/ngsbits/rohhunter/main.nf‎

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process NGSBITS_ROHHUNTER {
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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 "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2be56a07ac1d5a447a10fd061be4d6144620bec00bac834f58c2bdef0330147f/data'
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: 'community.wave.seqera.io/library/ngs-bits:2025_09--f6ea3a4494373ed6'}"
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input:
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tuple val(meta), path(vcf), path(exclude_bed)
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tuple val(meta2), path(annotation_beds)
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output:
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tuple val(meta), path("*.tsv"), emit: tsv
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tuple val("${task.process}"), val('ngsbits'), eval("RohHunter --version | sed 's/RohHunter //'"), topic: versions, emit: versions_ngsbits
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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 ann_beds = annotation_beds ? "-annotate ${annotation_beds.join(' ')}" : ''
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def excl_bed = exclude_bed ? "-exclude ${exclude_bed}" : ''
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"""
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RohHunter \\
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$args \\
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$ann_beds \\
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$excl_bed \\
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-out ${prefix}.tsv \\
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-in $vcf
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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echo $args
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touch ${prefix}.tsv
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"""
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}

‎modules/nf-core/ngsbits/rohhunter/meta.yml‎

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name: "ngsbits_rohhunter"
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description: RohHunter is a tool for run of homozygosity (ROH) detection based
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on a variant list in VCF format.
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keywords:
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- roh
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- homozygosity
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- allele frequency
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tools:
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- "ngsbits":
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description: "Short-read sequencing tools"
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homepage: "https://github.com/imgag/ngs-bits"
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documentation: "https://github.com/imgag/ngs-bits"
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tool_dev_url: "https://github.com/imgag/ngs-bits"
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licence:
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- "MIT"
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identifier: ""
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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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- vcf:
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type: file
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description: VCF file containing variants for ROH detection
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pattern: "*.vcf{,.gz}"
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ontologies:
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- edam: "http://edamontology.org/format_3016" # VCF
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- exclude_bed:
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type: file
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description: BED file with regions to exclude from ROH detection
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pattern: "*.bed"
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ontologies:
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- edam: "http://edamontology.org/format_3003" # BED
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- - meta2:
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type: map
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description: |
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Groovy Map containing annotation information
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e.g. `[ id:'sample1' ]`
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- annotation_beds:
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type: file
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description: BED file with annotation regions for ROH detection
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pattern: "*.bed"
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ontologies:
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- edam: "http://edamontology.org/format_3003" # BED
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output:
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versions_ngsbits:
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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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- ngsbits:
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type: string
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description: The name of the tool
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- RohHunter --version | sed 's/RohHunter //':
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type: eval
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description: The expression to obtain the version of the tool
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tsv:
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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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- "*.tsv":
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type: file
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description: TSV file containing the detected ROHs
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pattern: "*.tsv"
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ontologies:
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- edam: "http://edamontology.org/format_3475" # TSV
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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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- ngsbits:
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type: string
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description: The name of the tool
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- RohHunter --version | sed 's/RohHunter //':
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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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- "@nvnieuwk"
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maintainers:
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- "@nvnieuwk"

‎modules/nf-core/ngsbits/rohhunter/tests/main.nf.test‎

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nextflow_process {
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name "Test Process NGSBITS_ROHHUNTER"
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script "../main.nf"
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process "NGSBITS_ROHHUNTER"
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tag "modules"
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tag "modules_nfcore"
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tag "ngsbits"
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tag "ngsbits/rohhunter"
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topics "versions"
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test("homo_sapiens - vcf") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotc.vcf.gz', checkIfExists: true),
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[]
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]
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input[1] = [
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[ id: 'annotate_beds'],
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[]
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]
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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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process.out,
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topics
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).match() }
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)
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}
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}
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test("homo_sapiens - vcf & beds") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotc.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
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]
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input[1] = [
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[ id: 'annotate_beds'],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bins_10kb_annotated.bed', checkIfExists: true)
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]
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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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process.out,
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topics
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).match() }
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)
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}
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}
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test("homo_sapiens - vcf - 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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input[0] = [
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[ id:'test' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotc.vcf.gz', checkIfExists: true),
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[]
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]
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input[1] = [
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[ id: 'annotate_beds'],
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[]
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]
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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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process.out,
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topics
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).match() }
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)
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}
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}
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}

‎modules/nf-core/ngsbits/rohhunter/tests/main.nf.test.snap‎

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{
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"homo_sapiens - vcf": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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"test.tsv:md5,cb63516bae442eb91e59aec4d89a1d8f"
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]
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],
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"1": [
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[
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"NGSBITS_ROHHUNTER",
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"ngsbits",
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"2025_09"
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]
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],
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"tsv": [
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[
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{
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"id": "test"
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},
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"test.tsv:md5,cb63516bae442eb91e59aec4d89a1d8f"
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]
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],
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"versions_ngsbits": [
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[
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"NGSBITS_ROHHUNTER",
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"ngsbits",
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"2025_09"
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]
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]
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},
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{
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"versions": [
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[
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"NGSBITS_ROHHUNTER",
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"ngsbits",
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"2025_09"
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]
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]
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}
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],
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"timestamp": "2026-06-15T14:33:12.646074394",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "26.04.1"
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}
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},
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"homo_sapiens - vcf & beds": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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"test.tsv:md5,d45383ec2c0f62e28efaca8e8f5ff53e"
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]
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],
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"1": [
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[
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"NGSBITS_ROHHUNTER",
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"ngsbits",
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"2025_09"
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]
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],
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"tsv": [
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[
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{
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"id": "test"
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},
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"test.tsv:md5,d45383ec2c0f62e28efaca8e8f5ff53e"
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]
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],
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"versions_ngsbits": [
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[
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"NGSBITS_ROHHUNTER",
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"ngsbits",
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"2025_09"
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]
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]
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},
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{
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"versions": [
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[
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"NGSBITS_ROHHUNTER",
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"ngsbits",
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"2025_09"
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]
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]
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}
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],
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"timestamp": "2026-06-15T14:35:43.303225273",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "26.04.1"
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}
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},
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"homo_sapiens - vcf - stub": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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[
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"NGSBITS_ROHHUNTER",
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"ngsbits",
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"2025_09"
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]
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],
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"tsv": [
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[
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{
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"id": "test"
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},
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"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions_ngsbits": [
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[
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"NGSBITS_ROHHUNTER",
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"ngsbits",
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"2025_09"
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]
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]
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},
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{
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"versions": [
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[
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"NGSBITS_ROHHUNTER",
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"ngsbits",
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"2025_09"
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]
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]
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}
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],
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"timestamp": "2026-06-15T14:33:48.820950611",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "26.04.1"
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}
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}
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}

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