Monroe Bug Fix

This update fixes an issue where only one read pair was carried forward after iVar step.

Critical Monroe Bug Fix

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.

The Cecret release!

This update includes the 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

Monroe Cluster Report Bug Fix

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

Major bug fix

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.

Minor version tweak

No significant code changes.

Features and bug fixes

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.

Cutshaw release

Changes:

• added cutshaw workflow
• added mafft
• dryad index fix
• update to NCBI AMRFinder plus
• various bug fixes

Bug Fixes

Changes:

• Bash pipe bug fix
• Collision issue in trimmomatic workflows
• Report builder bug fix

better versioning

Changes:

• Version information is now displayed from help menu
• More output from update function