Staphb-toolkit

This release applies a fix for Monroe where iVar was not trimming primers correctly in the pe and se assembly workflows. This release is considered a critical bug fix because the issue has the potential to affect downstream analyses and had gone undiscovered for a period of time.

This update includes the [Cecret](https://github.com/UPHL-BioNGS/Cecret) workflow for analyzing SARS-CoV-2 sequences from the Illumina platform.

This update introduces the clear labs workflow for the Monroe pipeline!
This update introduces the single end workflow for the Monroe pipeline!

This update also includes the following bug fixes:
* Fixed task associated memory and CPU parameters
* Fixed install packaging from setup.py script
* Adjusted minimum read depth to call a variant in the pe_assembly and se_assembly Monroe pipeline to 10

Fixed an issue with Monroe Cluster Report failing when encountering a "/" in the fasta header

v1.2.2 had an issue with monroe's profile configuration that would prevent it from running. v1.2.4 fixes this issue.

Also updated how versioning is tracked simplifying toolkit releases.

No significant code changes.

This release adds the following:
* Updates to Monroe ONT pipeline to accommodate new ONT barcode kits.
* Update to allow local singularity images or other container repositories to be used in the toolkit.
* Dryad report tool path fix.
* Memory checking issues in various workflows.
* Fixes for default file name splitting.