Hello everyone,
I am creating a workflow with a tool that receives text as input.
These options allow me to give text as input inside the workflow creation. I am trying to change that with
“Simple inputs used for workflow logic” in order to provide the text input before running the workflow and not inside the workflow creation. I change the tool configuration like this:
This way does not allow me to connect the 2 tools inside the workflow.
Am I doing something wrong?
Thanks a lot!
Hi @tkarabatsis,
you need to click on the “Add connection to module” button on the right hand side:
A new input will appear then in the workflow editor to which you can connect your parameter.
Hello mvdbeek,
thanks a lot for the quick reply!
I changed the workflow with the way you told me and now it looks like this:
I try to run the workflow, I add the values from here:
but when I click Run Workflow, I get this error:
May 23 15:09:33 thanasis3 run.sh[5648]: galaxy.workflow.run ERROR 2019-05-23 15:09:33,103 Failed to schedule Workflow[id=42,name=Unnamed workflow], problem occurred on WorkflowStep[index=0,type=parameter_input].
May 23 15:09:33 thanasis3 run.sh[5648]: Traceback (most recent call last):
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 190, in invoke
May 23 15:09:33 thanasis3 run.sh[5648]: incomplete_or_none = self._invoke_step(workflow_invocation_step)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 266, in _invoke_step
May 23 15:09:33 thanasis3 run.sh[5648]: use_cached_job=self.workflow_invocation.use_cached_job)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/modules.py”, line 713, in execute
May 23 15:09:33 thanasis3 run.sh[5648]: progress.set_outputs_for_input(invocation_step, step_outputs)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 397, in set_outputs_for_input
May 23 15:09:33 thanasis3 run.sh[5648]: self.set_step_outputs(invocation_step, outputs)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 428, in set_step_outputs
May 23 15:09:33 thanasis3 run.sh[5648]: output=output,
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 432, in _record_workflow_output
May 23 15:09:33 thanasis3 run.sh[5648]: self.workflow_invocation.add_output(workflow_output, step, output)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/model/init.py”, line 4443, in add_output
May 23 15:09:33 thanasis3 run.sh[5648]: if output_object.history_content_type == “dataset”:
May 23 15:09:33 thanasis3 run.sh[5648]: AttributeError: ‘unicode’ object has no attribute ‘history_content_type’
May 23 15:09:33 thanasis3 run.sh[5648]: galaxy.workflow.run ERROR 2019-05-23 15:09:33,103 Failed to execute scheduled workflow.
May 23 15:09:33 thanasis3 run.sh[5648]: Traceback (most recent call last):
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 83, in __invoke
May 23 15:09:33 thanasis3 run.sh[5648]: outputs = invoker.invoke()
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 190, in invoke
May 23 15:09:33 thanasis3 run.sh[5648]: incomplete_or_none = self._invoke_step(workflow_invocation_step)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 266, in _invoke_step
May 23 15:09:33 thanasis3 run.sh[5648]: use_cached_job=self.workflow_invocation.use_cached_job)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/modules.py”, line 713, in execute
May 23 15:09:33 thanasis3 run.sh[5648]: progress.set_outputs_for_input(invocation_step, step_outputs)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 397, in set_outputs_for_input
May 23 15:09:33 thanasis3 run.sh[5648]: self.set_step_outputs(invocation_step, outputs)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 428, in set_step_outputs
May 23 15:09:33 thanasis3 run.sh[5648]: output=output,
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/workflow/run.py”, line 432, in _record_workflow_output
May 23 15:09:33 thanasis3 run.sh[5648]: self.workflow_invocation.add_output(workflow_output, step, output)
May 23 15:09:33 thanasis3 run.sh[5648]: File “/srv/executor/lib/galaxy/model/init.py”, line 4443, in add_output
May 23 15:09:33 thanasis3 run.sh[5648]: if output_object.history_content_type == “dataset”:
May 23 15:09:33 thanasis3 run.sh[5648]: AttributeError: ‘unicode’ object has no attribute ‘history_content_type’
Any ideas?
Yeah, that’s been fixed in https://github.com/galaxyproject/galaxy/pull/7799, I can open a PR to backport this.
That would be really helpful!
Thanks a lot!
