Arvados

This is probably related: The "Input your outputname to allelotype" parameter should be a text box. I've fixed it and didn't receive the error anymore.

However this issue should still stand because I tried to run GATK3 here: qr1hi-d1hrv-v3tb1ikn8isbbc5 on my bcosctemp@gmail.com and it still doesn't show which parameters I need to correct in order to run the pipeline.

I think it is failing because of the following component value:

output_prefix = {:required=>true, :dataclass=>"Collection", :title=>"Input your output name to allelotype", :default=>"test"}

I updated the method unreadable_inputs_present? in pipeline_instances_controller to checkout readable only for a pdh or uuid and the issue is now resolved.

However, do we want to do more such as check it is not "output" or "output_prefix" etc?

Peter said: as long as a non-empty string is provided for a Collection or File dataclass, we need to check readability. In this particular pipeline, there was a bug in the template where by mistake the output_prefix was configured as dataclass Collection; and hence disabling the Run button is the right behavior. Hence:

• Reverted the previous update. Also, updated to use red font in this case.

• Tested with qr1hi-d1hrv-80zon4obj9ufhvr

• I could not access qr1hi-d1hrv-v3tb1ikn8isbbc5 using my non-admin account.

• However, you can verify using instances in my shared folder if need be (you can be anonymous user): https://workbench.qr1hi.arvadosapi.com/pipeline_instances/qr1hi-d1hrv-z3ko667e07nkzk8