#2072 Add DOTSeq cell_cycle subset test data for modules Pull request opened by pinin4fjords Summary Test fixtures for nf-core/modules#11742 (`dotseq/dotseq`) under

data/genomics/homo_sapiens/riboseq_expression/dotseq/

. DOTSeq is a Bioconductor package for differential ORF usage (DOU) + ORF-level differential translation efficiency (DTE). Its API takes a featureCounts-format ORF count table plus a flattened ORF GTF/BED pair, so the existing

riboseq_expression/

salmon-gene-level fixtures don't satisfy the input contract. Rather than build new featureCounts + ORF annotations from the existing BAMs (which would require an ORF caller + featureCounts pass), this PR drops in the small

cell_cycle_subset

bundled with the DOTSeq package - DOTSeq's own example data, already in the exact shape its functions expect. Files | File | Size | Notes | | --------------------------------------- | ------ | --------------------------------------------------------------------------------------------------------------------------------------- | | featureCounts.cell_cycle_subset.txt.gz | 117 KB | ORF-level featureCounts output, 6644 ORF rows × 12 sample columns (chx-treatment subset of Ly et al. 2024) | | gencode.v47.orf_flattened_subset.gtf.gz | 81 KB | Flattened GENCODE v47 ORF annotation matching the count table, 6945 lines | | gencode.v47.orf_flattened_subset.bed.gz | 53 KB | Matching BED (6642 lines) | | metadata.txt.gz | 211 B | Headerless 24-sample metadata: run strategy replicate treatment condition | | samplesheet.csv | 423 B | Headered, chx-only subset of metadata.txt.gz (12 rows) - derived in this PR so the module can consume it without an extra header step | Total: 252 KB across 5 files. Why these specific files DOTSeq's

DOTSeqDataSetsFromFeatureCounts()

requires four inputs: 1.

count_table

with featureCounts annotation columns (

Geneid, Chr, Start, End, Strand, Length

) followed by per-sample counts. 2.

flattened_gtf

with

gene_id

+

exon_number

attributes (DOTSeq uses these to name ORFs as

gene_id:O###

). 3.

flattened_bed

matching the GTF. 4.

condition_table

with

run

,

strategy

,

replicate

,

condition

columns. The first four files are reused verbatim from DOTSeq's

inst/extdata/

.

samplesheet.csv

is the only derived file:

metadata.txt.gz

ships as a 5-column whitespace table with no header, so the module test would need to add a header before consuming it. To keep the nf-test minimal we ship the headered, chx-filtered version (12 rows matching the 12 sample columns in the featureCounts file) directly. Source & licence Bundled

inst/extdata

of compgenom/DOTSeq (Bioconductor 3.23 release). Upstream data is from Ly et al. 2024 (GSE231096 / SRR242304XX cell-cycle Ribo-seq + RNA-seq cohort), captured as the DOTSeq author's example dataset. Package licence: MIT. Test plan •

modules/nf-core/dotseq/dotseq/tests/main.nf.test

in nf-core/modules#11742 consumes these fixtures via

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

URLs pinned to this PR's branch; URLs to be updated to

modules

after this PR merges •

nf-core modules test --profile docker dotseq/dotseq

runs DOTSeq's DOU + DTE + per-strategy DESeq2 fits + plots end-to-end in ~4 min on a c5.9xlarge against this fixture set nf-core/test-datasets