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PMCC-BioinformaticsCore / janis-core

Core python modules for Janis Pipeline workflow assistant
GNU General Public License v3.0
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fromwdl: requires runtime.disks, yet that is optional in the spec #93

Closed mr-c closed 3 years ago

mr-c commented 3 years ago

https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#disks

Traceback (most recent call last):
  File "/home/michael/src/janis/janis-core/fromwdl.py", line 5, in <module>
    WdlParser.from_doc("/home/michael/wdl2cwl/wdl2cwl/tests/wdl_files/bowtie_1.wdl").translate();
  File "/home/michael/src/janis/janis-core/janis_core/ingestion/fromwdl.py", line 45, in from_doc
    tasks.append(parser.from_loaded_object(t))
  File "/home/michael/src/janis/janis-core/janis_core/ingestion/fromwdl.py", line 51, in from_loaded_object
    return self.from_loaded_task(obj)
  File "/home/michael/src/janis/janis-core/janis_core/ingestion/fromwdl.py", line 252, in from_loaded_task
    disk=self.parse_disk_requirement(rt.get("disks")),
  File "/home/michael/src/janis/janis-core/janis_core/ingestion/fromwdl.py", line 227, in parse_disk_requirement
    raise Exception(f"Couldn't recognise memory requirement '{value}'")
Exception: Couldn't recognise memory requirement 'None'

Should fall back to the default value of 1 GiB