New carrot updates requires updates to carrot_helper Template class and Test class

[bshifaw]

https://github.com/broadinstitute/gatk-sv/blob/ef29ea1374687bd62cfd18bd9e2905944256a4c8/carrot/carrot_helper.py#L699

The latest version of carrot provides the option for test and eval wdl dependencies. If running carrot_helper with the latest version of carrot the script will fail with "TypeError: __init__() got an unexpected keyword argument 'eval_wdl_dependencies'"

Adding eval_wdl_dependencies and test_wdl_dependencies should resolve the issue

class Template(BaseModel):
    """
    A carrot template is composed of WDL to be tested,
    a WDL that evaluates the tested WDL's output, and
    a set of inputs for both test and evaluation WDLs.
    """
    pipeline_id: str
    test_wdl: str
    test_wdl_checksum: str
    eval_wdl: str
    eval_wdl_checksum: str
    eval_wdl_dependencies: str
    test_wdl_dependencies: str
    results: List = field(default_factory=list)
    test: str = None

Similar issue with Test class https://github.com/broadinstitute/gatk-sv/blob/ef29ea1374687bd62cfd18bd9e2905944256a4c8/carrot/carrot_helper.py#L721 Error:

File "/home/bshifaw/test_carrot/wdl_test/carrot_helper.py", line 469, in create_test
    return Test(**response,
TypeError: __init__() got an unexpected keyword argument 'eval_option_defaults'

Fix:

class Test(BaseModel):
    template_id: str
    eval_input_defaults_checksum: str
    test_input_defaults_checksum: str
    template_path: str
    eval_option_defaults: dict = field(default_factory=dict)
    test_option_defaults: dict = field(default_factory=dict)
    eval_input_defaults: dict = field(default_factory=dict)
    test_input_defaults: dict = field(default_factory=dict)

Similar issue with Run class https://github.com/broadinstitute/gatk-sv/blob/ef29ea1374687bd62cfd18bd9e2905944256a4c8/carrot/carrot_helper.py#L730

File "/home/bshifaw/test_carrot/wdl_test/carrot_helper.py", line 565, in create_run
    return Run(**response, run_dir=os.path.join(
TypeError: __init__() got an unexpected keyword argument 'eval_options'

Fix

class Run(BaseModel):
    def __init__(self, name, test_id, test_cromwell_job_id,
                 eval_cromwell_job_id, status, finished_at,
                 test_input, eval_input, test_options, eval_options,, created_at, created_by,
                 errors=None, description=None, run_id=None, uuid=None,
                 results=None, run_dir=None):
        super().__init__(run_id or uuid, name, description,
                         created_at, created_by)
        self.test_id = test_id
        self.test_cromwell_job_id = test_cromwell_job_id
        self.eval_cromwell_job_id = eval_cromwell_job_id
        self.status = status
        self.finished_at = finished_at
        self.test_input = test_input
        self.eval_input = eval_input
        self.test_options = test_options
        self.eval_options = eval_options
        self.results = results
        self.run_dir = run_dir