try:
from generator.process import Process
except ImportError:
from assemblerflow.generator.process import Process
[docs]class Abricate(Process):
"""Abricate 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 = None
self.ignore_type = True
self.status_channels = ["STATUS_abricate"]
self.params = {
"abricateDatabases": {
"default": '["resfinder", "card", "vfdb", "plasmidfinder", '
'"virulencefinder"]',
"description": "Specify the databases for abricate."
}
}
self.link_start = None
self.link_end.append({"link": "MAIN_assembly",
"alias": "MAIN_assembly"})
self.directives = {
"abricate": {
"container": "ummidock/abricate",
"version": "0.8.0-1"
},
"process_abricate": {
"container": "ummidock/abricate",
"version": "0.8.0-1"
}
}
[docs]class Prokka(Process):
"""Prokka 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 = None
self.ignore_type = True
self.link_start = None
self.link_end.append({"link": "MAIN_assembly",
"alias": "MAIN_assembly"})
self.directives = {
"prokka": {
"cpus": 2,
"container": "ummidock/prokka-nf",
"version": "1.12.0-2"
}
}