This components runs the allele calling operation of ChewBBACA on a set of fasta samples to perform a cg/wgMLST analysis

Input/Output type

  • Input type: Fasta
  • Output type: None


The default input parameter for fasta data is --fasta.


  • chewbbacaQueue: Specifiy a queue/partition for chewbbaca. This option is only used for grid schedulers.
  • chewbbacaTraining: Specify the full path to the prodigal training file of the corresponding species.
  • schemaPath: The path to the chewbbaca schema directory.
  • schemaSelectedLoci: The path to the selection of loci in the schema directory to be used. If not specified, all loci in the schema will be used.
  • chewbbacaJson: If set to True, chewbbaca’s allele call output will be set to JSON format.
  • chewbbacaToPhyloviz: If set to True, the ExtractCgMLST module of chewbbaca will be executed after the allele calling.
  • chewbbacaProfilePercentage: Specifies the proportion of samples that must be present in a locus to save the profile.
  • chewbbacaBatch: Specifies whther a chewbbaca run will be performed on the complete input batch (all at the same time) or one by one.

Published results

  • results/chewbbaca_alleleCall: The results of the allelecall for each
  • results/chewbbaca: The cg/wgMLST schema prepared for phyloviz.

Published reports


Default directives

  • chewbbaca:
    • cpus: 4
    • container: mickaelsilva/chewbbaca_py3
    • version: latest
  • chewbbaca_batch:
    • cpus: 4
    • container: mickaelsilva/chewbbaca_py3
    • version: latest
  • chewbbacaExtractMLST:
    • container: mickaelsilva/chewbbaca_py3
    • version: latest