Automated bacteria characterization Workflow
Goal of this repository is to provided an automated workflow for Bacteria characterisation.
- a sample sheet linking sample name to Fastq files
- a metadata sheet containing sample information from LIMS (form to define)
- a config file describing execution parameters
- a QC table with acceptance criteria (species-wise)
- Assemblies
- QC check results
- cgMLST clusters, species-wise
- low priority: characterisation reports (AMR, Virulence, serotypes)
- Species-wise + global catalog of samples and metadata
- Export-ready tables for external comm (NRLs, EFSA, Land-DB)
- must be possible to not include samples in databases (comparison mode)
- must be possible to analyze a dataset independently of existing , e.g. for ring trials or validations(independant mode)
- sanity check inputs
- parse LIMS metadata
- run AQUAMIS on fastq
- compare QC results to acceptance criteria (AutoQC)
- produce an AutoQC report
- create a sample sheet with accepted samples
- run chewieSnake in compare or join mode (to be defined)
- check allel quality and refine sample sheet excluding bad sample
- merge samples in cgMLST databases
- LIMS parser
- AQUAMIS wrapper
- AutoQC
- chewieSnake wrapper
- export module