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.
Detailed documentation for workflows is available in the wiki.
[^1] Libuit, Kevin G., Emma L. Doughty, James R. Otieno, Frank Ambrosio, Curtis J. Kapsak, Emily A. Smith, Sage M. Wright, et al. 2023. “Accelerating Bioinformatics Implementation in Public Health.” Microbial Genomics 9 (7). https://doi.org/10.1099/mgen.0.001051.
