#2064 Add rpbp test data: per-stage intermediates for nf-core/modules#11695 Pull request opened by pinin4fjords Summary Test fixture set for nf-core/modules#11695 (the eight

rpbp/*

modules +

fasta_gtf_bam_rpbp

subworkflow) under

data/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 | File | Size | Notes | | ----------------------------------------------------------- | ------- | ----------------------------------------------------------------------------------------------------------------- | | reference.annotated.bed.gz | 234 KB | Transcript-level annotated BED from rpbp/preparegenome | | reference.orfs-genomic.annotated.bed.gz | 1.49 MB | Genomic-coordinate ORF BED from rpbp/preparegenome | | reference.orfs-exons.annotated.bed.gz | 1.33 MB | Exon-coordinate ORF BED from rpbp/preparegenome | | SRX11780888_chr20.metagene-profile.csv.gz | 53 KB | from rpbp/extractmetageneprofiles | | SRX11780888_chr20.metagene-periodicity-bayes-factors.csv.gz | 19 KB | from rpbp/estimatemetagenebayesfactors | | SRX11780888_chr20.periodic-offsets.csv.gz | <1 KB | from rpbp/selectperiodicoffsets | | SRX11780888_chr20.periodic_lengths_offsets.tsv | 68 B | from rpbp/getperiodiclengthsoffsets (lenient '10 1 None 0.0' thresholds; chr20 alone does not pass rpbp defaults) | | SRX11780888_chr20.profiles.mtx.gz | 331 KB | from rpbp/extractorfprofiles | | SRX11780888_chr20.bayes-factors.bed.gz | 602 KB | from rpbp/estimateorfbayesfactors | | README.md | <4 KB | Derivation recipe + per-file size/source. | Total: 4.1 MB across 10 files. Every file <4 MiB. Source Single

nf-core subworkflows test fasta_gtf_bam_rpbp

run on the existing chr20 cohort: • BAM:

aligned_reads/SRX11780888_chr20.bam

(+

.bai

) • FASTA:

Homo_sapiens.GRCh38.dna.chromosome.20.fa.gz

• GTF:

Homo_sapiens.GRCh38.111_chr20.gtf

(all from this same

riboseq_expression/

folder). rpbp version:

4.0.1

(Wave container `community.wave.seqera.io/library/rpbp:4.0.1--71297b462026e13b`). Test plan •

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

in nf-core/modules#11695 consume these fixtures via

<http://raw.githubusercontent.com|raw.githubusercontent.com>

URLs pinned to this branch; URLs to be updated to

modules

after this PR merges •

nf-core subworkflows test fasta_gtf_bam_rpbp

(the integration test) still runs the full chain end-to-end nf-core/test-datasets