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Description
While trying the workflow on the 'tiny_test', I got the following errors:
[job adaptor_trimming_and_qc_trimmed] Job error:
Error collecting output for parameter 'fastq1_trimmed':
CWL/tools/trim_galore.cwl:160:3: Traceback (most recent call last):
CWL/tools/trim_galore.cwl:160:3:
CWL/tools/trim_galore.cwl:160:3: File "/home/luna.kuleuven.be/u0120338/anaconda3/envs/conda_toil/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 539, in collect_output_ports
CWL/tools/trim_galore.cwl:160:3: compute_checksum=compute_checksum)
CWL/tools/trim_galore.cwl:160:3:
CWL/tools/trim_galore.cwl:160:3: File "/home/luna.kuleuven.be/u0120338/anaconda3/envs/conda_toil/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 652, in collect_output
CWL/tools/trim_galore.cwl:160:3: raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
CWL/tools/trim_galore.cwl:160:3:
CWL/tools/trim_galore.cwl:160:3: File "/home/luna.kuleuven.be/u0120338/anaconda3/envs/conda_toil/lib/python2.7/site-packages/schema_salad/sourceline.py", line 166, in exit
CWL/tools/trim_galore.cwl:160:3: raise self.makeError("\n".join(traceback.format_exception(exc_type, exc_value, tb)))
CWL/tools/trim_galore.cwl:160:3:
WorkflowException: CWL/tools/trim_galore.cwl:163:7: Traceback (most recent call last):
CWL/tools/trim_galore.cwl:163:7:
CWL/tools/trim_galore.cwl:163:7: File "/home/luna.kuleuven.be/u0120338/anaconda3/envs/conda_toil/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 652, in collect_output
CWL/tools/trim_galore.cwl:163:7: raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
CWL/tools/trim_galore.cwl:163:7:
CWL/tools/trim_galore.cwl:163:7: WorkflowException: Did not find output file with glob pattern: '[u'val_1.fq']'