chewbbaca

Purpose

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

Note

Software page: https://github.com/B-UMMI/chewBBACA

Input/Output type

• Input type: Fasta
• Output type: None

Note

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

Parameters

• 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

sample.

• results/chewbbaca: The cg/wgMLST schema prepared for phyloviz.

Published reports

None.

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