Question: Extending workflow from single file input to collection input
gravatar for johnathanwong4
25 days ago by
johnathanwong410 wrote:

So I've made a work flow with various tools on the toolshed. These tools can only take in a single file as input. Is there a way to wrap my workflow such that it works for a collection of inputs?

ADD COMMENTlink modified 24 days ago by Jennifer Hillman Jackson25k • written 25 days ago by johnathanwong410
gravatar for Jennifer Hillman Jackson
24 days ago by
United States
Jennifer Hillman Jackson25k wrote:


You can test out using a workflow that contains another workflow (aka "sub-workflow").


  1. Create a workflow (what you already have now). This will become a sub-workflow in the next steps. Make sure that it includes an "input" or you won't be able to link to it.
  2. Create the wrapping primary workflow. It should contain a "collection input" left at the default type (list). Then scroll down in the far left tool list to the Workflow section and click on the workflow from #1 above. It will appear on the workflow editing canvas the same as if you were adding a tool. Link the two with a noodle and save.
  3. Construct a dataset collection of type list in a history and test out your new primary workflow.

This may or may not work, it depends how those other tools were wrapped. If it doesn't work at some step, the tool wrappers you are using will need to be updated to accept collection inputs.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 24 days ago by Jennifer Hillman Jackson25k

Thanks. This solution my scenario.

ADD REPLYlink written 22 days ago by johnathanwong410

Good news and glad that worked! Jen

ADD REPLYlink written 21 days ago by Jennifer Hillman Jackson25k
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