Make pipeline robust to changing file naming conventions

[claraqin]

A generalization of Issue #23.

There are many places in the processing pipeline that attempt to parse information from the file name, or to store information in the file name. We should try to trim away these pieces, replacing them with a metadata-based identification system, which is now possible thanks to Lee's new version of downloadSequenceMetadata(). Some of these pieces are:

• remove_unmatched_files()
• retrieving all sequence run IDs at the beginning of the process_*_sequences.Rmd vignettes
• (potentially) all custom functions (e.g. qualityFilter16S(), trimPrimersITS()) that differentiate between forward and reverse sequence files by looking for a regex pattern in their filenames

[claraqin]

This is now being handled by the meta_reliant_utils branch

[claraqin]

Closed by merge pull request