Source code for flowcraft.generator.components.mlst

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." } }
[docs]class Metamlst(Process): """MetaMlst mapping process template interface This process is set with: - ``input_type``: reads - ``output_type``: None - ``ptype``: pre_assembly """ def __init__(self, **kwargs): super().__init__(**kwargs) self.input_type = "fastq" self.output_type = None self.directives = {"metamlst": { "container": "flowcraft/metamlst", "version": "1.1-1", "memory": "{4.Gb*task.attempt}" } } self.params = { "metamlstDB": { "default": "'/NGStools/metamlst/metamlstDB_2017.db'", "description": "Specify the metamlstDB (full path) for MLST checking." }, "metamlstDB_index": { "default": "'/NGStools/index/metamlstDB_2017'", "description": "Specify the Bowtie2 metamlstDB index (full path) for MLST checking." } }