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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
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Can't specify more than one pipeline per protocol #226

Closed stolarczyk closed 4 years ago

stolarczyk commented 4 years ago

in pipeline interface

tried this:

protocol_mapping:
  make_bed: [bedmaker, bedmaker1]
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.6/bin/looper", line 10, in <module>
    sys.exit(main())
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/looper.py", line 846, in main
    rerun=(args.command == "rerun"), **compute_kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/looper.py", line 335, in __call__
    max_cmds=args.lumpn, max_size=args.lump)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/looper.py", line 260, in process_protocols
    submission_bundles = prj.build_submission_bundles(proto)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/project.py", line 144, in build_submission_bundles
    this_protocol_pipelines.replace(";", ",") \
AttributeError: 'list' object has no attribute 'replace'

and this: 

protocol_mapping:
  make_bed: bedmaker, bedmaker1
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.6/bin/looper", line 10, in <module>
    sys.exit(main())
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/looper.py", line 846, in main
    rerun=(args.command == "rerun"), **compute_kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/looper.py", line 400, in __call__
    schema_file = piface.get_pipeline_schema(pipeline)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/pipeline_interface.py", line 594, in get_pipeline_schema
    schema_filepath = self.get_attribute(pipeline_name, "schema", path_as_list=False)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/pipeline_interface.py", line 499, in get_attribute
    config = self.select_pipeline(pipeline_name)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/pipeline_interface.py", line 618, in select_pipeline
    raise MissingPipelineConfigurationException(pipeline_name)
looper.exceptions.MissingPipelineConfigurationException: bedmaker, bedmaker1