mhoban / rainbow_bridge

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Add more blast options #74

Closed mhoban closed 1 month ago

mhoban commented 4 months ago

Right now the user can only specify so many options to the blastn command. We ought to expand that so they can pass any option.

Is it possible to just get any option that starts with '--blast-' and use whatever comes after that as the named option to blast? This would be a good way to do this without having to explicitly address all the available options. So for instance if they passed --blast-import_search_strategy, we would call blastn with -import_search_strategy

mhoban commented 4 months ago

We can keep the ones we already have for ease of use but expand this feature to cover any others.

mhoban commented 3 months ago

This should do the trick:

blast_params = params.findAll {it.key =~ /^blast-/}.collect { k, v -> "-${k.tokenize('-')[1]} ${v}" }
mhoban commented 1 month ago

Done and merged