VGP- unable to select or add hind3 restriction enzyme to Hi-C scaffolding workflow

[HT87]

Hello,

I noticed that VGP Hi-C scaffolding workflow does provide few selections for restriction enzyme input and does not allow a custom input. I used HindIII in my Hi-C library which have recognition site on AAGCTT.
However, i can not input that to VGP Hi-C scaffolding workflow.

Any advice or help to resolve that would be appreciated.

Thank you

[jennaj]

Welcome, @HT87

You can add in a custom input for this option – let me show you how to do this with that exact step!

I’m going to list all the steps to hopefully make this clear, and please ask followup questions.

1. Import the workflow into your account

   For the workflow: VGP Scaffolding-HiC-VGP8
   Where to source inside a Galaxy Tutorial
   Where to source at Dockstore

2. Open the workflow in the Editor

   Galaxy Tutorials → Hands-on: Creating, Editing and Importing Galaxy Workflows / Creating, Editing and Importing Galaxy Workflows / Using Galaxy and Managing your Data

3. Locate the target tool

In the screenshot, I followed the input for the “Preconfigured enzymes”, and found that it connected to the YAHS tool. Then I clicked on the YAHS tool in the canvas, and that action brought up the tool’s parameter settings in the right panel.

5. Review the available options for the parameter

Screenshot of the available parameter settings.

5. Change the parameter setting

Screenshot after the new parameter setting is selected: Enter a specific sequence. Notice that this is a free-text entry field. You could modify the workflow directly here and save, but that doesn’t make the workflow very reusable!

6. Toggle the option to add in a new input to the workflow

Screenshot of where to set the toggle to instead add in a new place for a distinct input to this tool, and the workflow itself! This will be a new text file that will be selected when the workflow is run.

Screenshot of the YAHS tool on the canvas, after that option is toggled.

7. Adjust the workflow inputs to match your new parameter settings!

   • Remove any inputs that are now disconnected from any tools.
   • Add in new inputs for any newly required input datasets, and be sure to name them in a useful way!
   • Connect your new inputs to the tools you changed.
   • Note: if you modified an input to be a collection inputs type, or to not be a collection, you may need to disconnected and reconnect other noodles in your workflow, especially the noodles downstream from the tool you modified. Why? To reset the metadata inside your workflow to accommodate the new data structures!
   • Save your workflow with a distinct name, and consider updating the workflow description to remind yourself (and others) about what is different!.

8. Test your updated workflow!

9. Bonuses

• More options for using custom workflow parameters are here: Galaxy Tutorial → Hands-on: Using Workflow Parameters / Using Workflow Parameters / Using Galaxy and Managing your Data

• You can also add in graphics to the workflow canvas using the palette functions. Examples of what that can look like are in these screenshots, and other places. This is entirely custom, and a great way to annotate details: where and what, exactly! Galaxy Tutorial → Hands-on: Creating high resolution images of Galaxy Workflows / Creating high resolution images of Galaxy Workflows / Using Galaxy and Managing your Data.

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Please give that a try