GEMSTONE Workflows
WDL workflows for the GEMSTONE project. Includes workflows to process Illumina paired-end reads from isolates and plate swipes. These workflows are based on the PHB workflows by Theiagen[^1]. Workflows for useful standalone tools are also provided, namely StrainGE for strain level detection, Kraken/Bracken2 for abundance estimation, and metaWRAP for MAG binning and refinement.
This repository also contains DOCKERFILE files for bespoke Docker images used in some WDL tasks.
This is a companion discussion topic for the original entry at github.com/marcoteix/gemstone-workflows/GEMSTONE_StrainGR