WorkflowException: Expression evaluation error: No JSON object could be decoded

mdibl / biocore_analysis

A root directory for Biocore pipeline analysis

GNU General Public License v3.0

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WorkflowException: Expression evaluation error: No JSON object could be decoded #5

Closed nathanielmki closed 5 years ago

nathanielmki commented 5 years ago

Currently debugging my edited fastqc cwl commandlinetool, modified from pitagora's fastqc. I have added error and console logging, and am receiving the above error when I run the tool.

nathanielmki commented 5 years ago

I receive the error whether or not I run with a JSON file or YAML. Additionally, downstream of the WorkflowException, I get fastqc.cwl:12:1: TypeError: Cannot read property 'replace' of undefined

nathanielmki commented 5 years ago

There was a mismatch in the input types between the JSON and CWL files. Resolved this mismatch, fastqc.cwl is currently running