Minor Bug Fix

Updated staphb-tk to appropriately display a workflow's help table even if a description is missing in the workflow's schema.

StaPH-B Toolkit v2

Version 2 of the StaPH-B Toolkit provides an overhaul of how workflows are packaged and containerized applications are accessed. Version 2 allows for dynamic fetching of the workflows so both the latest versions as well as previous versions of the workflows are always available. The Toolkit also now has the ability to select specific versions of Nextflow allowing a greater control over how the workflows are run. Updates to the Toolkit's application list and workflows are now served through GitHub making it easier for workflows and applications to be added without needing to update the toolkit itself. Additionally there have been some UI tweaks to make using applications and tools a bit easier.

Overall version 2 seeks to improve access to workflows by improving both the user experience and reducing the effort of contributors.

Changelog

• Combined the staphb-tk and staphb-wf commands into a single command: staphb-tk
• Incorporated workflow version selection and nextflow version selection
• Added workflow help
• Improved UI for readability and accessibility
• Updated documentation
• Many minor process tweaks

Update Cecret v.2.4.20220407

1.3.10

1.3.10

Update Cecret to v.2.3.20220114

1.3.9

1.3.9

Update Cecret to 2.2.20211221

1.3.8

1.3.8

Updating Cecret Version to v.2.0.2021115

Lots of great updates to Cecret including Nextstrain fix. Read more here:
https://github.com/UPHL-BioNGS/Cecret/releases/tag/2.0.2021115

Updating Cecret Version to v.1.2.20210930

1.3.6

1.3.6

Updates to Cecret

Cecret updates to fix issues with NextClade and VADR.

Major Workflow Updates and Fixes

This one took awhile!

• Cecret
  • Bug Fixes
  • Updates for Pangolin V3
  • Configuration file changes
• Monroe
  • Updates for Pangolin V3
• Monroe ONT
  • Removed barcode prefix to allow broader naming schemes
• Dryad
  • Bug Fixes
  • Added mlst formatting process
  • Added mapping and coverage processes
  • Updated amrfinder_summary

Workflow Updates

Cecret Updates:

• process ivar_variants and ivar_consensus have memory designations so that it doesn't fail as often
• process samtools_plot_ampliconstats has been added
• process vadr has been added
• process bedtools has been renamed to bedtools_multicov and now requires the user to supply the amplicon file (instead of me trying to imagine what it would be from the primer bedfile)
• ivar variants now creates a pseudo vcf file for bamsnap.
• --annotation has been added an option, just in case the end user wants to run pangolin, nextclade, vadr, mafft/snpdists/iqtree on a collection of fastas
• process filter has been added
• most processes now have a free text *_options parameter to make it easier for the end user to modify options
• container and stageInMode have been added to processes in the main file
• renaming files now has an external as opposed to internal script
• I've adjusted the config file template into something that makes more sense to me and added more variables

Monroe ONT Updates

• Removed Nanopolish option
• Updated ARTIC workflow and added Medaka models
• Option to use reads that are already basecalled and de-multiplexed