Question: scatter over optional argument
0
gravatar for ionox0
7 days ago by
ionox0120
ionox0120 wrote:

Is it possible to scatter over an optional argument (of type string[]?) when the argument isn’t provided?

The message that I get from cwltool when trying this is:

[workflow standard_bam_generation] starting step module_1
Unhandled exception
Traceback (most recent call last):
  File "/home/johnsoni/virtualenvs/pipeline_test/lib/python2.7/site-packages/cwltool-1.0.20180306140409-py2.7.egg/cwltool/workflow.py", line 401, in try_make_job
    emptyscatter = [shortname(s) for s in scatter if len(inputobj[s]) == 0]
cwl • 58 views
ADD COMMENTlink modified 7 days ago • written 7 days ago by ionox0120

Is there a reason you don't provide the argument? It seems like you should include it if you want to use it as an input. The error is returning that you are scattering over nothing.

ADD REPLYlink written 7 days ago by drkennetz260

I want to be able to provide an array of adapter sequences to scatter over (string[]: [adapter1, adapter2, ...]), but if the adapters are not provided I would like to be able to provide another argument to the tool to specify it to use the default illumina adapter (string: --illumina), in which case I'd like the scatter to be ignored.

ADD REPLYlink written 5 days ago by ionox0120

Is the string you want to scatter over an output from a previous step?

ADD REPLYlink written 7 days ago by drkennetz260

No it's not an output from a previous step

ADD REPLYlink written 5 days ago by ionox0120
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