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ENCODE-DCC / croo

Cromwell output organizer
MIT License
13 stars 3 forks source link

Link/copy stdout and stderr files? #35

Closed davetang closed 3 years ago

davetang commented 3 years ago

Hi there,

thank you so much for croo; it does exactly what I need. I was just wondering if there is a way to refer to the stdout and stderr files generated by Cromwell in the output JSON file, so that they can be copied/linked to the output directory?

Cheers, Dave

leepc12 commented 3 years ago

No, croo does not keep the original directory structure including stdout/stderr files in it. You need to manually parse metadata_json["calls"] object. Each call object has stdout and stderr. Or use gsutil ls or find -name stdout.

davetang commented 3 years ago

OK, I'll write a separate script to parse the metadata file. Thanks!