Add DOTSeq cell_cycle subset test data for modules#2072
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Bundled inst/extdata files from the DOTSeq Bioconductor package, copied into homo_sapiens/riboseq_expression/dotseq for use by the nf-core/modules dotseq/dotseq nf-test: - featureCounts.cell_cycle_subset.txt.gz: ORF-level featureCounts output - gencode.v47.orf_flattened_subset.gtf.gz: flattened ORF annotation - gencode.v47.orf_flattened_subset.bed.gz: matching BED - metadata.txt.gz: sample condition table (run/strategy/replicate/treatment/condition) Source: https://github.com/compgenom/DOTSeq, MIT license.
Derived from metadata.txt.gz, filtered to treatment=chx samples (which is what the bundled featureCounts table contains) and headered as run,strategy,replicate,condition for direct consumption by the dotseq/dotseq nf-test.
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Companion to nf-core/modules#11742 - the dotseq module nf-test 404s on this samplesheet URL until this PR merges, otherwise green. |
Document the file set, derivation, and verification of the DOTSeq cell_cycle_subset fixtures, matching the gedi/price test data PR convention.
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Lets CI verify the module is actually green; revert this commit once nf-core/test-datasets#2072 merges and the canonical modules-branch URL resolves.
Replaces the upstream featureCounts table and flattened GTF/BED with a tidy per-ORF count matrix (counts.tsv.gz) and per-ORF annotation TSV (annotation.tsv.gz) so the dotseq module can call DOTSeqDataSetsFromSummarizeOverlaps() directly. ORF identifiers and sample columns are preserved; both files are derived from the same DOTSeq cell_cycle_subset cohort. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Aligns the module's input contract with deltate / anota2seq so that consumers can dispatch between the three ORF-DTE methods without maintaining a separate prep step for dotseq. The four featureCounts/GTF/BED inputs collapse to a per-ORF count matrix (orf_id + sample columns) plus a per-ORF annotation TSV (orf_id + gene_id + optional orf_type/coords). The R template now calls DOTSeqDataSetsFromSummarizeOverlaps() and builds the required GRanges in-process from the annotation TSV; the model fit, contrast tables, and plotDOT outputs are unchanged. Test fixtures updated alongside in nf-core/test-datasets#2072 (commit 8c9b27c). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Test fixtures for nf-core/modules#11742 (
dotseq/dotseq) underdata/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 smallcell_cycle_subsetbundled with the DOTSeq package - DOTSeq's own example data, already in the exact shape its functions expect.Files
featureCounts.cell_cycle_subset.txt.gzgencode.v47.orf_flattened_subset.gtf.gzgencode.v47.orf_flattened_subset.bed.gzmetadata.txt.gzrun strategy replicate treatment conditionsamplesheet.csvmetadata.txt.gz(12 rows) - derived in this PR so the module can consume it without an extra header stepTotal: 252 KB across 5 files.
Why these specific files
DOTSeq's
DOTSeqDataSetsFromFeatureCounts()requires four inputs:count_tablewith featureCounts annotation columns (Geneid, Chr, Start, End, Strand, Length) followed by per-sample counts.flattened_gtfwithgene_id+exon_numberattributes (DOTSeq uses these to name ORFs asgene_id:O###).flattened_bedmatching the GTF.condition_tablewithrun,strategy,replicate,conditioncolumns.The first four files are reused verbatim from DOTSeq's
inst/extdata/.samplesheet.csvis the only derived file:metadata.txt.gzships 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/extdataof 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.testin nf-core/modules#11742 consumes these fixtures viaraw.githubusercontent.comURLs pinned to this PR's branch; URLs to be updated tomodulesafter this PR mergesnf-core modules test --profile docker dotseq/dotseqruns DOTSeq's DOU + DTE + per-strategy DESeq2 fits + plots end-to-end in ~4 min on a c5.9xlarge against this fixture set