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ga4gh / fasp-scripts

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Google Cloud Pipeline jobs composed in python fail #2

Closed ianfore closed 3 years ago

ianfore commented 3 years ago

Pipeline job composed in python submitted via pipelines().run fails. See runstats() method in gcpls_samtools.py

The parameters for the run match those for a job submitted via the command line. The details appear to be the same in task list interface.

For now the workaround is to submit the job via subprocess.run()

ianfore commented 3 years ago

Determined the problem was with how the command line was submitted. Elements of the command line must be submitted as a list of strings rather than a single string. Fix was committed here