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EBI-Metagenomics / workflow-is-cwl

This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts
https://www.elixir-europe.org/
Apache License 2.0
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Validating the complete assembly workflow #32

Closed arnaudmeng closed 5 years ago

arnaudmeng commented 5 years ago

I'm working on the complete workflow validation. I've difficulties to figure out how to fix the issue below. Any idea ?

Tool definition failed validation: ../workflow-is-cwl-assembly/workflows/TranscriptomeAssembly-wf.cwl:155:5: Type property "['null', 'seq_type']" not a valid Avro schema: Union item must be a valid Avro schema: Could not make an Avro Schema object from seq_type.

Runned command :

cwltool --validate ../workflow-is-cwl-assembly/workflows/TranscriptomeAssembly-wf.cwl ../workflow-is-cwl-assembly/workflows/TranscriptomeAssembly-wf.test.job.paired-end.yaml

mscheremetjew commented 5 years ago

@arnaudmeng This should be fixed now. I just pushed the fix to the assembly branch. Can you please test and close the ticket if it works!?

arnaudmeng commented 5 years ago

@mscheremetjew Thank you ! It now works, with the last push you've made I obtain a valid cwltools definition.

Command: cwltool --validate ../workflow-is-cwl-assembly/workflows/TranscriptomeAssembly-wf.cwl TranscriptomeAssembly-wf.test.job.paired-end.yaml

Result: (...) ../workflow-is-cwl-assembly/workflows/TranscriptomeAssembly-wf.cwl is valid CWL.