Add workflow/script parameter "vector_type" -- now available as a variable to use in the report template. Options are "ssaav", "scaav", or "unspecified".
Extract new script create_report.R from report.Rmd (#17)
Update the main workflow for reusability and parallelism (via @bcantarel )
Add a test status shield to README
Update test files (downsampled BAMs, mini host genome, renamed files and folders)
Code cleanup
Rename output files from .csv and flipflop_assignments.txt to tsv, for uniformity (they were already tab-separated internally)
create_report.Rfromreport.Rmd(#17)