I am attempting to edit a workflow that has multiple sub-workflows. The problem is that after I edit it, the edits look like they are holding, but then when I run the workflow it is still applying the original parameters. If I download and then upload, my edits disappear. I am trying to edit the Main Metatranscriptomics workflow: (Workflows / Metatranscriptomics analysis using microbiome RNA-seq data / Microbiome) and the only two changes I am trying to make are: 1) change filter options in cutadapt to a minimum length of 74 instead of 150, 2) change input options for MetaPhlAn2 to deselect “profile viral organisms” (default is to include) and to ignore eukaryotic organisms (need to change to column select for this option). Any suggestions? I am able to edit the sub-workflows individually and save those edits if I save as separate workflows, but I am unable to save the overall workflow incorporating the sub-workflow edits.
The problem is that after I edit it, the edits look like they are holding, but then when I run the workflow it is still applying the original parameters.
Hello and welcome @kam132!
After a subworkflow is updated, the main WF has no way of knowing! SubWF changes are only propogated to the main WF when you explicitly request it. You can either:
- update the main workflow or
- individually update the relevant subworkflows on the main workflow
then save the main WF and it should run the updated subWF as you expect?
This is probably a dumb question, but so how do I update the main workflow then if it is composed of sub workflows?
Use that gear icon to expose the upgrade workflow option. That’s the most complete and certain way to upgrade everything - subworkflows and tools - to their latest versions - beware that you don’t break something that way?
For individual controlled updates, select each subWF one at a time - that exposes two arrows in a circle - an option to reload that subWF - same goes for tools if an updated version is available.
Thank you so much!