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nf-core / metapep

From metagenomes to epitopes and beyond
https://nf-co.re/metapep
MIT License
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Check supported models and handle warnings #48

Closed skrakau closed 1 year ago

skrakau commented 1 year ago

Description of feature

Check if requested alleles and lengths combinations are supported by epitope prediction tools and handle warnings/errors properly!

Given in MERGE_PREDICTIONS_BUFFER.out.ch_prediction_warnings, use and output directly!

tillenglert commented 1 year ago

Another check for the module lengths is introduced in PR #75

tillenglert commented 1 year ago

The peptide length will be checked for an available model and if multiple alleles are given only the matching models are used and the user is informed that the prediction will happen at reduced peptide length (e.g. for mouse alleles H2-Db and H2-Ld: H2-Db is available at length 9 and H2-Ld is available at length 8 and 9. Only peptides of length 9 will be predicted)

This will be implemented as extra process.

@skrakau Should I check in this process if the alleles are available and remove it from check_samplesheet_create_tables?

tillenglert commented 1 year ago

related to https://github.com/nf-core/metapep/issues/74