Workflow Taxonomy Options not available

I’m currently trying to run the NCBI Foreign Contamination Screen workflow from the tutorial but on my own samples. Every time I import the workflow the advanced options don’t let me change the taxonomy. The first time I ran it as the hands on tutorial and was able to select the taxonomy but now it is locked on fungi budding yeasts. Any ideas on how to fix this so I can run my A. baumannii isolate data through the same workflow?
Tutorial link for reference:

Hi @Brianna_Eales

That input choice is “free text”. Meaning, there isn’t a pre-computed listing to choose from, and the existing setting can’t be replaced on the workflow runtime form.

Instead, you’ll need to look up what you want to use for this parameter, then type it into the workflow editor, then save, then run.


You other option is to extract a workflow from the a history that already has the option modified.

I’m not sure if the way this works can be improved or not. Do you have any suggestions @mvdbeek ?


The GTN has a bunch of workflow tutorials that are worth reviewing. It sounds like you are importing the workflow each time you want to run it – that is Ok but you can also edit what you have, make copies, customize and run from that view instead.

Hope this helps, and thanks for including the tutorial link for context! :slight_smile:

Thank you so much for this!

So following your instructions I know where to put the div, but when I first ran it there was a drop down menu for all of them and so I don’t remember what exactly to write for free text that will match what it’s supposed to.

Does that make sense?

1 Like

Yes, I’m not sure if the best way either. Let’s wait for Marius to reply. It might be a day of wait due to time differences.

The other option is to run the tool in a history with the settings you want to use, extract a workflow from it, open it in the editor, see what is entered – maybe even copy it out – then modify your full workflow.

Whew! that sounds awful but I can’t think of another way. There is something about this tool getting in the way but I’m not sure yet where the change should be: with the tool itself, some index file, or the workflow editor. And, it might a combination of factors. Marius will probably know what to do since he is our workflow master!

Thanks so much! I was just trying to see if I could get it to work and decided to use the tax ID instead but I’m not sure if I put it in the correct format :grimacing: so we will see.

Thanks again!