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Question: Extending workflow from single file input to collection input
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gravatar for johnathanwong4
5 weeks ago by
johnathanwong4 • 10
johnathanwong4 • 10 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?

workflow sub-workflow nested-workflows galaxy • 76 views
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modified 5 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 5 weeks ago by johnathanwong4 • 10
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gravatar for Jennifer Hillman Jackson
5 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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

Steps:

  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 COMMENT • link written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k
1

Thanks. This solution worked.in my scenario.

ADD REPLY • link written 5 weeks ago by johnathanwong4 • 10

Good news and glad that worked! Jen

ADD REPLY • link written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k
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