common-workflow-language
cwl_utils.errors.JavascriptException: NodeJSEngine requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it.
Hi Team
I am trying to check if the pipeline is free from errors and I ran the validate command from the folder where the.cwl file is. I am getting java error as mentioned below. Has it to do with the version of the cwl? Could you please help me out?
Workflow Code
cwltool --validate --debug atac-seq-noumi-pe.cwl
Full Traceback
(base) katarij1@C02F602BMD6W atac_seq % cwltool --validate --debug atac-seq-noumi-pe.cwl INFO /opt/anaconda3/bin/cwltool 3.1.20221115160822 INFO Resolved 'atac-seq-noumi-pe.cwl' to 'file:///Users/katarij1/Projects/Gaurav/ATAC/CWL_scripts-master/workflows/atac_seq/atac-seq-noumi-pe.cwl' ERROR I'm sorry, I couldn't load this CWL file. The error was: Traceback (most recent call last): File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/main.py", line 1158, in main tool = make_tool(uri, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/load_tool.py", line 619, in make_tool tool = loadingContext.construct_tool_object(processobj, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/workflow.py", line 54, in default_make_tool return Workflow(toolpath_object, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/workflow.py", line 108, in init self.make_workflow_step( File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/workflow.py", line 155, in make_workflow_step return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/workflow.py", line 250, in init self.embedded_tool = load_tool(toolpath_object["run"], loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/load_tool.py", line 641, in load_tool return make_tool(uri, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/load_tool.py", line 619, in make_tool tool = loadingContext.construct_tool_object(processobj, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/workflow.py", line 54, in default_make_tool return Workflow(toolpath_object, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/workflow.py", line 108, in init self.make_workflow_step( File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/workflow.py", line 155, in make_workflow_step return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/workflow.py", line 250, in init self.embedded_tool = load_tool(toolpath_object["run"], loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/load_tool.py", line 641, in load_tool return make_tool(uri, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/load_tool.py", line 619, in make_tool tool = loadingContext.construct_tool_object(processobj, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/workflow.py", line 50, in default_make_tool return command_line_tool.CommandLineTool(toolpath_object, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/command_line_tool.py", line 403, in init super().init(toolpath_object, loadingContext) File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/process.py", line 710, in init validate_js_expressions( File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/validate_js.py", line 240, in validate_js_expressions expression_lib_line_errors, expression_lib_line_globals = jshint_js( File "/opt/anaconda3/lib/python3.9/site-packages/cwltool/validate_js.py", line 165, in jshint_js returncode, stdout, stderr = exec_js_process( File "/opt/anaconda3/lib/python3.9/site-packages/cwl_utils/sandboxjs.py", line 576, in exec_js_process return cast(Tuple[int, str, str], _exec_js_process(*args, **kwargs)) File "/opt/anaconda3/lib/python3.9/site-packages/cwl_utils/sandboxjs.py", line 196, in exec_js_process new_proc = self.new_js_proc( File "/opt/anaconda3/lib/python3.9/site-packages/cwl_utils/sandboxjs.py", line 396, in new_js_proc raise JavascriptException( cwl_utils.errors.JavascriptException: NodeJSEngine requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it. Tried nodejs, node, docker run node:slim
Your Environment
- cwltool version: /opt/anaconda3/bin/cwltool 3.1.20221115160822
NodeJSEngine requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it. Tried nodejs, node, docker run node:slim
I believe you are missing node. Try installing it with a package manager like conda, apt-get or brew and re-running the command.
