Include FASTA parameter, stage REF_CACHE and export REF_PATH

[cduong11]

Attempt to address issue #137

• Enable the option to pass a FASTA file to SAMTOOLS_MERGE to avoid the lookup behaviour of samtools.
• Generate the REF_PATH variable based on the original process outlined here using the seq_cache_populate.pl script.

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[cduong11]

Hi @tkchafin, this approach is my proposal for handling CRAM files with samtools. It ensures that the reference FASTA is not retrieved multiple times and prevents errors when working with aligned CRAM inputs. Let me know if you'd like any further changes!