v4.0

What's Changed

• version4.0 release by @slsevilla in #18

Full Changelog: v3.1...v4.0

v3.1

What's Changed

• updated CI by @slsevilla in #14
• docs: update to match ci changes by @slsevilla in #15
• merging changes into dev by @slsevilla in #16
• Updates to cecret, pangolin, nextclade by @slsevilla in #17

Full Changelog: v2.2...v3.1

v3.0

What's Changed

• updated CI by @slsevilla in #14
• docs: update to match ci changes by @slsevilla in #15
• merging changes into dev by @slsevilla in #16
• Updates to cecret, pangolin, nextclade by @slsevilla in #17

Full Changelog: v2.2...v3.0

v2.2

What's Changed

• Dev by @slsevilla in #13
• style updates, GISAID metadata handling updates

Full Changelog

v2.1...v2.2

v2.1

Final release before changing AWS instances

v2.0

Pipeline updated:

• Cecret2.0
• Pangolin v4.1
• Nextclade v2.4.0

Cecret moved from staph-tk to sourcing from GitHub

v1.1

Version to include Cecret, GISAID and NCBI uploading

v1.0

CECRET workflow v1.0

• takes config file parameters
• downloads analysis and FASTQ files from BASESPACE using CLI
• runs CECRET pipeline
• runs QC report
• removes temporary files, merges batched results