dev

v4.0

Update Cecret, Pangolin, Nextclade
Updates to config handling

v3.1

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

v3.0

updated CI by @slsevilla in #14
docs: update to match ci changes by @slsevilla in #15
merging changes into dev by @slsevilla in #16

v2.2

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

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