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
: 4container
: mickaelsilva/chewbbaca_py3version
: latest
chewbbaca_batch
:cpus
: 4container
: mickaelsilva/chewbbaca_py3version
: latest
chewbbacaExtractMLST
:container
: mickaelsilva/chewbbaca_py3version
: latest