pyview_test_data/MS_LSM/progs/finalize_pipeline.py

from view.python_core.processing_pipelines import PipelineManager

# this tells view all settings including the folder structure of your project
# On Windows, if you copy paths from the file explorer, make sure the string below is always of the form r"......"
ymlfile = r"/home/aj/SharedWithWindows/view_test_data/MS_LSM/usage_lsm.yml"

# specify the pipeline definition file to use
pipelines_definition_file \
    = r"/home/aj/SharedWithWindows/view_test_data/MS_LSM/progs/pipelines_settings/processing_pipelines.yml"

# specify the animals whose data is to be processed; and their corresponding pipelines
animals = {
    # "<animal name>": <pipeline name>,
    "2020_02_06_OK107_GCaMP6f": 'pipeline2'
}


for animal, pipeline2finalize in animals.items():

    pipeline_manager = PipelineManager(project_yml_file=ymlfile, animal=animal,
                                       pipelines_config_file=pipelines_definition_file)
    pipeline_manager.finalize_pipeline(pipeline2finalize)