#2050 Add SRP254919.propd_grea_test_sets.gmt for nf-core/differentialabundance Pull request opened by pinin4fjords Summary Adds

testdata/SRP254919.propd_grea_test_sets.gmt

- a small Ensembl-id gmt with two synthetic gene sets drawn from the first 50 gene IDs of

SRP254919.salmon.merged.gene_counts.top1000cov.tsv

. Why For nf-core/differentialabundance to test

propd

+

grea

end-to-end (see differentialabundance#724) we need a gmt that uses the same gene IDs as the abundance matrix.

propr/grea

operates directly on the adjacency matrix's row/column names (Ensembl IDs in this dataset) without any symbol↔️id translation step, so the existing gene-symbol-based

mh.all.v2022.1.Mm.symbols.gmt

would produce empty gene sets. The two sets are synthetic (just chunks of the first 50 IDs), so they exercise the code path but carry no biological signal - in line with the existing minimal-test-data convention. Test plan • Once merged, the differentialabundance

test_rnaseq_propd_grea

profile (introduced in nf-core/differentialabundance#XXX) references this file via

<https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/SRP254919.propd_grea_test_sets.gmt>

. nf-core/test-datasets