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feat(rpbp/extractorfprofiles): add module (#11959)
* feat(rpbp/extractorfprofiles): add module [skip ci] * ci: trigger tests * test(rpbp/extractorfprofiles): fix test-data path and assert output content Point inputs at params.modules_testdata_base_path (nf-core/test-datasets, modules branch) instead of a deleted personal-fork branch that 404s and fails CI on every profile. Switch the real test to snapshot(process.out).match(). The output is deterministic across cpu counts and byte-identical between the conda and container toolchains, so the content snapshot guards against regressions and matches the convention across the rpbp series. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(tests): add sanitizeOutput to test snapshots [skip ci] Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix(tests): strip numeric snapshot keys stripped by sanitizeOutput [skip ci] Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix(rpbp/extractorfprofiles): move descriptor into default prefix per nf-core convention Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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‎modules/nf-core/rpbp/extractorfprofiles/environment.yml‎

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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::rpbp=4.0.1

‎modules/nf-core/rpbp/extractorfprofiles/main.nf‎

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process RPBP_EXTRACTORFPROFILES {
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tag "$meta.id"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/14/146c3f15abf184a5ec13531d2a040ba7b9235c1091723aa37c7a119817411367/data' :
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'community.wave.seqera.io/library/rpbp:4.0.1--71297b462026e13b' }"
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input:
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tuple val(meta), path(bam), path(bai), path(lengths_offsets)
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tuple val(meta2), path(orfs_genomic_bed)
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tuple val(meta3), path(exons_bed)
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output:
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tuple val(meta), path("${prefix}.mtx.gz"), emit: profiles
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tuple val("${task.process}"), val('rpbp'), eval('python -c "import rpbp; print(rpbp.__version__)"'), emit: versions_rpbp, topic: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}.profiles"
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"""
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LENGTHS=\$(tail -n +2 ${lengths_offsets} | cut -f1 | tr '\\n' ' ')
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OFFSETS=\$(tail -n +2 ${lengths_offsets} | cut -f2 | tr '\\n' ' ')
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extract-orf-profiles \\
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${bam} \\
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${orfs_genomic_bed} \\
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${exons_bed} \\
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${prefix}.mtx.gz \\
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--lengths \$LENGTHS \\
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--offsets \$OFFSETS \\
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--num-cpus ${task.cpus} \\
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${args}
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"""
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stub:
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prefix = task.ext.prefix ?: "${meta.id}.profiles"
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"""
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echo "" | gzip > ${prefix}.mtx.gz
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"""
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}

‎modules/nf-core/rpbp/extractorfprofiles/meta.yml‎

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name: "rpbp_extractorfprofiles"
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description: |
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Build a per-ORF P-site count vector for every candidate open reading
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frame (ORF) in the catalogue. For each ORF, walks the spliced exons
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in 3-nucleotide codon steps and counts the P-site positions
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(read 5'-end coordinate plus the length-specific offset selected
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upstream) that fall in each codon. Counts are summed across all read
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lengths that passed the periodicity filter from
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`rpbp/getperiodiclengthsoffsets`.
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The resulting per-ORF vectors are the input to Bayesian translation
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scoring in `rpbp/estimateorfbayesfactors`: a translated ORF should
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show P-site density concentrated at codon-start positions, while a
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non-translated region should look flat or noisy. Emitted as a sparse
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matrix (one row per ORF, columns indexed by codon position).
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keywords:
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- rpbp
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- orf
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- psite
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- profile
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- riboseq
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tools:
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- "rpbp":
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description: "Rp-Bp - Bayesian inference of ribosome profiling data for identifying translated open reading frames"
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homepage: "https://github.com/dieterich-lab/rp-bp"
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documentation: "https://rp-bp.readthedocs.io"
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tool_dev_url: "https://github.com/dieterich-lab/rp-bp"
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doi: "10.1093/nar/gkw1350"
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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, e.g. `[ id:'sample1' ]`.
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- bam:
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type: file
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description: Sorted Ribo-seq BAM.
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pattern: "*.bam"
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ontologies: []
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- bai:
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type: file
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description: BAM index.
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pattern: "*.bai"
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ontologies: []
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- lengths_offsets:
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type: file
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description: Per-read-length offsets TSV from `rpbp/getperiodiclengthsoffsets`.
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pattern: "*.periodic_lengths_offsets.tsv"
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ontologies: []
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- - meta2:
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type: map
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description: |
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Groovy Map identifying the reference (e.g. `[ id:'reference' ]`).
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- orfs_genomic_bed:
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type: file
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description: Per-ORF genomic BED from `rpbp/preparegenome`.
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pattern: "*.orfs-genomic.annotated.bed.gz"
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ontologies: []
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- - meta3:
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type: map
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description: |
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Groovy Map identifying the reference (e.g. `[ id:'reference' ]`).
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- exons_bed:
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type: file
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description: Per-ORF exons BED from `rpbp/preparegenome`.
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pattern: "*.orfs-exons.annotated.bed.gz"
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ontologies: []
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output:
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profiles:
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- - meta:
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type: map
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description: Groovy Map inherited from input meta.
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- "${prefix}.mtx.gz":
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type: file
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description: Per-ORF P-site profile sparse matrix.
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pattern: "*.mtx.gz"
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ontologies: []
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versions_rpbp:
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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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- rpbp:
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type: string
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description: The name of the tool
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- python -c "import rpbp; print(rpbp.__version__)":
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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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- rpbp:
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type: string
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description: The name of the tool
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- python -c "import rpbp; print(rpbp.__version__)":
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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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- "@pinin4fjords"
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maintainers:
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- "@pinin4fjords"

‎modules/nf-core/rpbp/extractorfprofiles/tests/main.nf.test‎

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nextflow_process {
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name "Test Process RPBP_EXTRACTORFPROFILES"
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script "../main.nf"
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process "RPBP_EXTRACTORFPROFILES"
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tag "modules"
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tag "modules_nfcore"
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tag "rpbp"
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tag "rpbp/extractorfprofiles"
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test("homo_sapiens chr20 - extract orf profiles") {
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when {
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process {
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"""
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input[0] = Channel.of([
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[ id:'test', single_end:true, strandedness:'forward' ],
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam.bai", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/rpbp/SRX11780888_chr20.periodic_lengths_offsets.tsv", checkIfExists: true)
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])
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input[1] = [
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[ id:'reference' ],
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/rpbp/reference.orfs-genomic.annotated.bed.gz", checkIfExists: true)
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]
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input[2] = [
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[ id:'reference' ],
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/rpbp/reference.orfs-exons.annotated.bed.gz", 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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assertAll(
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{ assert process.success },
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{ assert snapshot(sanitizeOutput(process.out)).match() }
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)
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}
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}
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test("homo_sapiens chr20 - extract orf profiles - 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] = Channel.of([
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[ id:'test', single_end:true, strandedness:'forward' ],
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam.bai", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/rpbp/SRX11780888_chr20.periodic_lengths_offsets.tsv", checkIfExists: true)
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])
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input[1] = [
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[ id:'reference' ],
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/rpbp/reference.orfs-genomic.annotated.bed.gz", checkIfExists: true)
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]
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input[2] = [
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[ id:'reference' ],
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/rpbp/reference.orfs-exons.annotated.bed.gz", 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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assertAll(
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{ assert process.success },
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{ assert snapshot(sanitizeOutput(process.out)).match() }
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)
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}
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}
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}

‎modules/nf-core/rpbp/extractorfprofiles/tests/main.nf.test.snap‎

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{
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"homo_sapiens chr20 - extract orf profiles - stub": {
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"content": [
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{
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"profiles": [
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[
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{
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"id": "test",
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"single_end": true,
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"strandedness": "forward"
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},
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"test.profiles.mtx.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
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]
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],
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"versions_rpbp": [
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[
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"RPBP_EXTRACTORFPROFILES",
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"rpbp",
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"4.0.1"
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]
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]
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}
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],
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"timestamp": "2026-06-10T16:44:43.898520726",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "26.04.3"
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}
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},
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"homo_sapiens chr20 - extract orf profiles": {
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"content": [
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{
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"profiles": [
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[
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{
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"id": "test",
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"single_end": true,
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"strandedness": "forward"
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},
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"test.profiles.mtx.gz:md5,7e1ca4eecd50b189f5f4fc362a896d8b"
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]
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],
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"versions_rpbp": [
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[
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"RPBP_EXTRACTORFPROFILES",
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"rpbp",
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"4.0.1"
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]
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]
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}
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],
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"timestamp": "2026-06-10T16:44:38.531400548",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "26.04.3"
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}
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}
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}

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