enable the ability to create generic consensus genomes

[katrinakalantar]

Description

This PR makes it possible to create a generic consensus genome using the wdl workflow by passing the appropriate inputs (reference genome and primer files) and making the filterReads step optional. To generate generic consensus genomes, you would now need to include "filter_reads": false in the .json of wdl inputs.

note: this PR does not add additional error handling logic to ensure that a reference genome is of the correct format (.fasta) or any additional error handling.

Tests

• Tested locally on several different viruses and verified that the results look appropriate via comparison to ground truth genomes.
• Tested on staging using the run_sfn.py script. In particular, I tested that 1. it works with a "generic" non-sars-cov-2 reference genome (tested CHKV genome) and 2. verified that it still generates the same results for two different sars-cov-2 samples - one with PE inputs using ARTIC v3 and one with SE inputs using MSSPE.

[jshoe]

Just FYI @katrinakalantar, if you wanted to consolidate the "committer" appearance, you can run something like this locally so that the email is recognized by Github:

git config --global user.name "John Doe"
git config --global user.email johndoe@example.com