Add rpbp test data: per-stage intermediates for nf-core/modules#11695#2064
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Add rpbp test data: per-stage intermediates for nf-core/modules#11695#2064pinin4fjords wants to merge 1 commit into
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The rpbp module tests in nf-core/modules need their immediate-upstream inputs as static fixtures rather than chaining the six upstream stages of the rpbp pipeline (PREPAREGENOME -> EXTRACTMETAGENEPROFILES -> ESTIMATEMETAGENEBAYESFACTORS -> SELECTPERIODICOFFSETS -> GETPERIODICLENGTHSOFFSETS -> EXTRACTORFPROFILES -> ESTIMATEORFBAYESFACTORS). With these fixtures, each module test fetches one file rather than re-running the chain, cutting per-module test time from minutes to seconds. Fixtures derived from a single fasta_gtf_bam_rpbp subworkflow run on the existing chr20 BAM/FASTA/GTF in this folder. All files <4 MiB, ~4.1 MB total. See data/.../rpbp/README.md for full derivation. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Two interleaved changes: 1. Split the periodic-length filter (`get_periodic_lengths_and_offsets`) out of `rpbp/extractorfprofiles` into its own `rpbp/getperiodiclengthsoffsets` module. `extractorfprofiles` now takes a `lengths_offsets` TSV input rather than computing the filter inline. The threshold args move from `ext.args2` on `extractorfprofiles` to `ext.args` on `getperiodiclengthsoffsets`. `fasta_gtf_bam_rpbp` chains the new module between `selectperiodicoffsets` and `extractorfprofiles`. 2. Module-level tests now fetch their single immediate-upstream input from `nf-core/test-datasets:modules` (under `data/genomics/homo_sapiens/riboseq_expression/rpbp/`, added in nf-core/test-datasets#2064) instead of chaining six upstream stages in setup. Each module test runs in well under a minute. The subworkflow integration test still runs the full chain end-to-end. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Test fixture set for nf-core/modules#11695 (the eight
rpbp/*modules +fasta_gtf_bam_rpbpsubworkflow) underdata/genomics/homo_sapiens/riboseq_expression/rpbp/.Previously each rpbp module test in nf-core/modules chained six upstream stages (
PREPAREGENOME -> EXTRACTMETAGENEPROFILES -> ESTIMATEMETAGENEBAYESFACTORS -> SELECTPERIODICOFFSETS -> GETPERIODICLENGTHSOFFSETS -> EXTRACTORFPROFILES -> ESTIMATEORFBAYESFACTORS) in its setup just to produce its single immediate-upstream input. That was slow (several minutes per module on CI) and made module tests harder to debug. With these fixtures every module test fetches one static file and runs in well under a minute. The full chain is still exercised once, in the subworkflow integration test.Files
reference.annotated.bed.gzrpbp/preparegenomereference.orfs-genomic.annotated.bed.gzrpbp/preparegenomereference.orfs-exons.annotated.bed.gzrpbp/preparegenomeSRX11780888_chr20.metagene-profile.csv.gzrpbp/extractmetageneprofilesSRX11780888_chr20.metagene-periodicity-bayes-factors.csv.gzrpbp/estimatemetagenebayesfactorsSRX11780888_chr20.periodic-offsets.csv.gzrpbp/selectperiodicoffsetsSRX11780888_chr20.periodic_lengths_offsets.tsvrpbp/getperiodiclengthsoffsets(lenient'10 1 None 0.0'thresholds; chr20 alone does not pass rpbp defaults)SRX11780888_chr20.profiles.mtx.gzrpbp/extractorfprofilesSRX11780888_chr20.bayes-factors.bed.gzrpbp/estimateorfbayesfactorsREADME.mdTotal: 4.1 MB across 10 files. Every file <4 MiB.
Source
Single
nf-core subworkflows test fasta_gtf_bam_rpbprun on the existing chr20 cohort:aligned_reads/SRX11780888_chr20.bam(+.bai)Homo_sapiens.GRCh38.dna.chromosome.20.fa.gzHomo_sapiens.GRCh38.111_chr20.gtf(all from this same
riboseq_expression/folder).rpbp version:
4.0.1(Wave containercommunity.wave.seqera.io/library/rpbp:4.0.1--71297b462026e13b).Test plan
modules/nf-core/rpbp/*/tests/main.nf.testin nf-core/modules#11695 consume these fixtures viaraw.githubusercontent.comURLs pinned to this branch; URLs to be updated tomodulesafter this PR mergesnf-core subworkflows test fasta_gtf_bam_rpbp(the integration test) still runs the full chain end-to-end