#1987 Add 500-protein human SwissProt subset for mhcquant SDRF test Pull request opened by jonasscheid Summary Adds

testdata/UP000005640_9606_500prot.fasta

, a 500-protein subset of the human SwissProt proteome (UP000005640), for use as the default FASTA in the upcoming

test_sdrf

profile in nf-core/mhcquant. Rationale The current full proteome (

UP000005640_9606.fasta

, 20,610 proteins) causes the CometAdapter step in the SDRF test to exceed the 6 GB CI memory cap or hit the 2 h wall-time when combined with unspecific cleavage on the

PXD009752

test RAW files. Benchmarking showed the 500-protein subset: • Reduces CometAdapter wall-time from ~35 min to ~3 min per file (at

spectrum_batch_size=20000

) • Keeps peak RSS within the 6 GB cap • Still yields ~100 peptides at q<0.01 FDR, giving Percolator enough targets to train a stable SVM Content • First 500 entries of

UP000005640_9606.fasta

(deterministic head) • 329 KB (vs 13.6 MB for the full proteome) Related Used by nf-core/mhcquant#445 (SDRF/PRIDE input support). nf-core/test-datasets