Add runHMMER function for HMMER analysis

[AbhirupaGhosh]

These functions will be added to data_processing.R once approved.

The scripts are modifications of @epbrenner 's hmmering and rhmmer.

Description

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• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

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[jananiravi]

It looks like you moved a line -- unless I'm missing something, it's good to merge!

[jananiravi]

I see that I commented on one commit earlier -- sorry about that!

In principle, it looks good. I would like to request @eboyer221 or @epbrenner to run this locally and suggest non-alpine placeholders to ensure this works for all!

[charmvang]

Just had a thought, we have to run each HMMER database in the function separately and then combine the outputs later?

[jananiravi]

From @charmvang

Just had a thought, we have to run each HMMER database in the function separately and then combine the outputs later?

@AbhirupaGhosh, do we integrate these results and return a single df/parquet following the individual runs? 🤔

[eboyer221]

From @charmvang

Just had a thought, we have to run each HMMER database in the function separately and then combine the outputs later?

@AbhirupaGhosh, do we integrate these results and return a single df/parquet following the individual runs? 🤔

Confirmed with @AbhirupaGhosh that the multi-database aggregation is going to be a separate follow-up PR rather than part of this one. .runHMMER keeps a single database_path for now and users call it once per database.