Hi everyone. I’m looking at describing a workflow for (initially) checking the quality of genome sequences. I have written a series of Python scripts that do things like making decisions on parts of the workflow to run, calling command line tools, passing files to the next stages, etc, that would appear to be easier to do in CWL. However, I’m having some trouble with figuring out how to do the non-basic stuff. The User Guide gives nice examples of individual stages, and a simple workflow, but it’s hard to figure out all of the options that are possible.

For example, I think the scatter option will allow me to provide a series of input files, and it will perform the same steps in a workflows on each file. Later on, I want to then check ALL of the outputs to make sure they pass sanity checks before moving on to later stages (not yet defined). Do you have a workflow example that describes this? It’s not overly clear how it works exactly. I also have a step that might need repeating, depending on the output of later stages. In my example, FastQC is run on a file, and the output is checked for warn/fail flags depending on the defined tolerances. Some files may need to go through a quality trim stage, and then go back through the FastQC and checking stages, with second runthroughs deciding if a borderline original file is now okay to pass through. Is that kind of automated decision making possible in CWL?