Screening assembled genomes for contamination using NCBI FCS workflow not working

[jennaj]

Hi @Dibya

You won’t need to do that, you can use the workflow, you’ll just need to update it. See the topic I linked. I included a screenshot that shows exactly where to find the tool form Versions menu in the workflow editor. It is the same as a tool form, but the editor is new to some people, so I though it might be helpful.

Here, I’ll copy it

this

@jennaj

We might be able to correct the older version but it isn’t a priority. Full details are in here if you aren’t sure how to do this (screenshots, FAQs) → Correcting errors with NCBI FCS GX Foreign Contamination Screening assembled genomes

Points to

@jennaj

What to do

If you are working at UseGalaxy.org (where I was testing) the most current version is Galaxy Version 0.5.5+galaxy1 for three of the tools included, and the adaptor tool didn’t change and is still at Galaxy Version 0.5.0+galaxy0.

I was able to simply update the tool version in the GTN workflow, save, and run without any complicated changes to the parameters. This works about the same as the tool form directly. Open the workflow in the editor, click on the tool, modify the version(s), double check parameters are OK (new params, defaults), save, and run.

• FAQ: Changing the tool version

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Please give that a try and let us know if you need more help!

You should give this a try too. Learning how to make small modifications to workflows is really important. Tools change over time, servers may host slightly different versions (as in this case), you may want to use a different reference genome at some point in some workflow, or you may want to extract and create your own. These are really powerful and once you explore it you’ll see it is pretty much like a history but flattened out all at once. Really nice for planning your steps, too.

Let us know how this works!