def generate_analysis_tasks_and_snakefile(dataSet: dataset.MERFISHDataSet,
parametersFile: TextIO) -> str:
print('Generating analysis tasks from %s' % parametersFile.name)
analysisParameters = json.load(parametersFile)
snakeGenerator = snakewriter.SnakefileGenerator(analysisParameters,
dataSet, sys.executable)
snakefilePath = snakeGenerator.generate_workflow()
print('Snakefile generated at %s' % snakefilePath)
return snakefilePath
def test_snakemake_generator_one_task(simple_merfish_data):
taskDict = {
'analysis_tasks': [{
'task': 'SimpleAnalysisTask',
'module': 'merlin.analysis.testtask',
'parameters': {}
}]
}
generator = snakewriter.SnakefileGenerator(taskDict, simple_merfish_data)
workflow = generator.generate_workflow()
outputTask = simple_merfish_data.load_analysis_task('SimpleAnalysisTask')
assert not outputTask.is_complete()
snakemake.snakemake(workflow)
assert outputTask.is_complete()
shutil.rmtree('.snakemake')
def test_snakemake_generator_task_chain(simple_merfish_data):
taskDict = {
'analysis_tasks': [{
'task': 'SimpleAnalysisTask',
'module': 'merlin.analysis.testtask',
'analysis_name': 'Task1',
'parameters': {}
}, {
'task': 'SimpleParallelAnalysisTask',
'module': 'merlin.analysis.testtask',
'analysis_name': 'Task2',
'parameters': {
'dependencies': ['Task1']
}
}, {
'task': 'SimpleParallelAnalysisTask',
'module': 'merlin.analysis.testtask',
'analysis_name': 'Task3',
'parameters': {
'dependencies': ['Task2']
}
}]
}
generator = snakewriter.SnakefileGenerator(taskDict, simple_merfish_data)
workflow = generator.generate_workflow()
outputTask1 = simple_merfish_data.load_analysis_task('Task1')
outputTask2 = simple_merfish_data.load_analysis_task('Task2')
outputTask3 = simple_merfish_data.load_analysis_task('Task3')
assert not outputTask1.is_complete()
assert not outputTask2.is_complete()
assert not outputTask3.is_complete()
snakemake.snakemake(workflow)
assert outputTask1.is_complete()
assert outputTask2.is_complete()
assert outputTask3.is_complete()
shutil.rmtree('.snakemake')