Added --plus for no --organism option in amrfinder step

This release includes an added parameter (plus), which provides results from the AMRFinderPlus "--plus" option. This includes genes such as virulence factors, stress-response, etc in AMRFinderPlus' output. Additionally, incorrect paths hardcoded into the test_full profile option were corrected, and a Tower yaml file was added. Finally, the README was updated with descriptions for the inputs and parameters.

This release fixes the "NO FILE" error thrown in AWS when the default Kraken database is used. Note: this error only appeared in AWS, not when run locally.

This release updates the Kraken summary to allow for a custom database and fixes a data type error during the Kraken summary process

This release converts Spriggan to Nextflow DSL 2

This release fixes a minor error in the print statement for --test

This release features minor improvements to the bbduk, kraken, coverage, quast and amrfinder summary steps

This release features an updated trimming approach that trims from both ends of the read and preserves more data. This allows for greater coverage and better contigs than the previous sliding window approach. The summary output also now includes database versions for Kraken and NCBI AMR Finder Plus.