AutoBak

Automated bacteria characterization Workflow

Goal of this repository is to provided an automated workflow for Bacteria characterisation.

Requirements

Inputs

• 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)

Outputs

• 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)

Other reqs

• 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)

Workflow

• 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

Modules

• LIMS parser
• AQUAMIS wrapper
• AutoQC
• chewieSnake wrapper
• export module