Ideally you could do with collections what @jxtx showed for regular datasets (two or more datasets going into an input that accepts multiple datasets). It does become ambiguous if you try to do this with collections (should the input collections be fully consumed and you get a single output dataset, or treated element-wise and you get a single output collection back). If element-wise, should we iterate over the top level collection or the lowest level collection ?)
There is one trick that should work now. You can use the
Zip Collection tool, which will create a list of pairs from your two VCF collections. You can then use the
Apply Rule to Collection tool where you can take this list of pairs collection as input, click
edit in the tool form, and then click
Add / Modify Column Definitions. Click on
Add Definition ->
List Identifier and select column A, then click on
Assign another column and select column B. Click on Apply, Save and run the tool. You’ll get a list of lists, where the inner list contains 2 elements, one for each variant caller. You can use this list in bcftools concat to get a single collection of combined VCFs.
Unfortunately the user interface in the workflow editor doesn’t let you do this at the moment, but you can extract this operation from the history. I’ve done this here: https://usegalaxy.org/u/marius/w/workflow-constructed-from-history-test-1.
Hope that helps!