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Resolve "Enhance Input Run Format / Parsing"

aknecht2 requested to merge 12-enhance-input-run-format-parsing into master

Closes #12 (closed) The only thing I left out is the add species to genome information. The genome id's are just strings so a user could add species information there IF they really wanted i.e. grch38p6_human. It's information that doesn't need to be validated and is never used so it seemed unnecessary to include it.

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