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[FEATURE] Print useful help messages for typos in CLI arguments

Open fabianegli opened this issue 3 months ago • 1 comments

Description of feature

I just ran quantms with the argument '--add-decoy' instead of '--add-decoys' and it ran compute intensive steps until percolator failed and the computations had to be rerun. It would be nice if this kid of typos would result in an immediate failure with a useful help message immediately after invoking nextflow.

fabianegli avatar Sep 26 '25 06:09 fabianegli

Actually, I thougth we fixed that @daichengxin @jpfeuffer ? If not, @fabianegli feel free to add an step that checks if the databases includes decoy, it could be a simple grep script that check for the decoy prefix in the DB, before starting.

ypriverol avatar Sep 26 '25 06:09 ypriverol