common-workflow-language
Schema already in use error
Hello,
Trying to run a complex workflow that involves multiple nested imports and multiple subworkflows.
I am unsure when an import needs to be placed in the schema definition requirement.
The workflow validates and packs successfully however generates the following error when run:
Traceback (most recent call last):
File "/usr/local/lib/cwltool-3.0.20201203173111/schema_salad/avro/schema.py", line 409, in __init__
items_schema = make_avsc_object(items, names)
File "/usr/local/lib/cwltool-3.0.20201203173111/schema_salad/avro/schema.py", line 635, in make_avsc_object
return RecordSchema(
name, namespace, fields, names, atype, doc, other_props
)
File "/usr/local/lib/cwltool-3.0.20201203173111/schema_salad/avro/schema.py", line 535, in __init__
NamedSchema.__init__(self, schema_type, name, namespace, names, other_props)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/cwltool-3.0.20201203173111/schema_salad/avro/schema.py", line 255, in __init__
new_name = names.add_name(name, namespace, self)
File "/usr/local/lib/cwltool-3.0.20201203173111/schema_salad/avro/schema.py", line 218, in add_name
raise SchemaParseException(fail_msg)
schema_salad.avro.schema.SchemaParseException: The name "dragen-qc-coverage" is already in use.
Workflow (zipped): https://github.com/umccr/cwl-ica/releases/download/dragen-wgts-dna-pipeline%2F4.4.4__20251015010222/dragen-wgts-dna-pipeline__4.4.4__20251015010222.zip
Stderr logs: cwltool-already-in-use-debug-log.zip
Related: https://cwl.discourse.group/t/complex-workflow-cannot-be-packed/1022
This issue has been mentioned on Common Workflow Language Discourse. There might be relevant details there:
https://cwl.discourse.group/t/complex-workflow-cannot-be-packed/1022/2
@alexiswl That's a very old version of cwltool and presumably schema-salad as well. Is the error reproducible with the latest release of both?
Yes, agreed it's an old version but it's the one that ICA has stuck with.
Yes I have been able to do reproduce this with the latest version of cwltool as well.
If a full reprex would be useful, I can try write something with some dummy input json values?
This issue has been mentioned on Common Workflow Language Discourse. There might be relevant details there:
https://cwl.discourse.group/t/complex-workflow-cannot-be-packed/1022/4
If a full reprex would be useful, I can try write something with some dummy input json values?
Yes, please