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Add metabolomics test data for metaproviz modules - #2281
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rbartelme
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Sep 18, 2026
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Summary
Adds test data for the upcoming
metaproviz/*modules, under a new top-levelmetabolomics/folder.Why a new
metabolomics/folderDiscussed in nf-core Slack #modules, since no metabolomics test data existed yet. Following the same reasoning genomics uses (organize by data type, not by tool/software, for discoverability and reusability), we settled on
metabolomics/raw_annotation_data/rather than a tool-specificdelete_me/metaproviz/folder, since this data format (a feature-by-sample data matrix, sample metadata, and feature metadata) is a standard shape in metabolomics generally, not something specific to our modules.Structure:
metabolomics/raw_annotation_data/<cellline|patient>/<dataset>/, each with adata_matrix.csv,feature_matrix.csv, andsample_matrix.csv(the standard TSV/CSV shape), plus anSE.RDatafile (see below for why).Future additions can follow the same data-type-based convention, e.g.
metabolomics/raw_spectral_data/ormetabolomics/biocrates_data/for other metabolomics data shapes.Why both
SE.RDataand CSV files for the same dataOur modules accept two mutually exclusive input shapes: a Bioconductor
SummarizedExperiment(.rds), or the three flat files directly (data_matrix/feature_matrix/sample_matrix). Both are real, separately tested code paths, so we need real test data in both shapes to cover them. We considered only bundling theSummarizedExperimentobject, but that'sR-specific, so we kept the plain CSV/TSV files as the primary, standard, language-independent format, and added the
.rdsalongside it specifically to also exercise our modules'SummarizedExperimentinput path in testing.PR checklist
README.mdREADME.mdis still up-to-date (n/a, we only added new data, didn't modify any existing files)