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Create log file and handle various issues

Shanna Rucker requested to merge generate_outputs into shinyapp

Created write_log() function. Function uses tryCatch() to capture errors and warnings produced by other functions. write_log() applied to various other functions in RunPeakFQ observeEvent.

Also, resolved a few issues, most notably getting the site information read from spec file and written into spec file.

Merge ready to move forward after Sophia's review.

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