try:
from generator.process import Process
except ImportError:
from flowcraft.generator.process import Process
[docs]class Mlst(Process):
"""Mlst mapping process template interface
This process is set with:
- ``input_type``: assembly
- ``output_type``: None
- ``ptype``: post_assembly
It contains one **secondary channel link end**:
- ``MAIN_assembly`` (alias: ``MAIN_assembly``): Receives the last
assembly.
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.input_type = "fasta"
self.output_type = "fasta"
self.directives = {"mlst": {
"container": "ummidock/mlst",
}}
self.params = {
"mlstSpecies": {
"default": "null",
"description":
"Specify the expected species for MLST checking."
}
}
[docs]class Chewbbaca(Process):
"""Chewbbaca process template interface
This process is set with:
- ``input_type``: assembly
- ``output_type``: None
- ``ptype``: post_assembly
It contains one **secondary channel link end**:
- ``MAIN_assembly`` (alias: ``MAIN_assembly``): Receives the last
assembly.
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.input_type = "fasta"
self.output_type = None
self.ignore_type = True
self.link_start = None
self.link_end.append({"link": "MAIN_assembly",
"alias": "MAIN_assembly"})
self.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"
}
}
self.params = {
"chewbbacaQueue": {
"default": "null",
"description":
"Specifiy a queue/partition for chewbbaca. This option"
" is only used for grid schedulers."
},
"chewbbacaTraining": {
"default": "null",
"description":
"Specify the full path to the prodigal training file "
"of the corresponding species."
},
"schemaPath": {
"default": "null",
"description":
"The path to the chewbbaca schema directory."
},
"schemaSelectedLoci": {
"default": "null",
"description":
"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."
},
"schemaCore": {
"default": "null",
"description": ""
},
"chewbbacaJson": {
"default": "false",
"description":
"If set to True, chewbbaca's allele call output will be "
"set to JSON format."
},
"chewbbacaToPhyloviz": {
"default": "false",
"description":
"If set to True, the ExtractCgMLST module of chewbbaca"
" will be executed after the allele calling.",
},
"chewbbacaProfilePercentage": {
"default": 0.95,
"description":
"Specifies the proportion of samples that must be "
"present in a locus to save the profile."
},
"chewbbacaBatch": {
"default": "false",
"description":
"Specifies whether a chewbbaca run will be performed on the"
" complete input batch (all at the same time) or one by "
"one."
}
}