Open louperelo opened 1 year ago
@louperelo Is that with cwltool
or a different CWL engine?
It is with cwltool
.
I try to call the pipeline with cwltool pipeline.cwl runs.yml
There is a longer conversation on DataPlant Teams about the two issues I am having at the moment.
Does type: double?
behave differently?
No, it unfortunately behaves the same as with type: float?
.
This is a cwltool bug; we will fix it and add a new conformance test! https://github.com/common-workflow-language/cwltool/issues/1831
Great news! Thank you @mr-c!
A new release of cwltool
is out, with the fix: https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20230424211314 a.k.a. https://pypi.org/project/cwltool/3.1.20230424211314/
PROBLEM
CWL converts all numbers smaller than 1e-5 to a string, even if the default is given as a number (0.00001)
gives this error:
It does not happen for floats >0.0001, though. Also, negative numbers in the default are passed as a string.
SOLUTION
Define these numbers as strings in the
.cwl
file, e.g.:TASK
The defaults taken from the
nextflow_schema.json
have either to be checked if they are <0.0001 and if so, written to the.cwl
file asstring?
OR all input taken from the.json
has to be written as astring?
in the.cwl
.