Is there a way to run upto a particular step in a workflow?

I see the --target option that lets you start from a particular step in a workflow. But is there a way to run a cwl workflow only upto a particular step ?

One could use an input/output with target to restrict which steps to run. But what if the step you want to run has no inputs/outputs corresponding to the top level ones, i.e. it uses/produces only intermediate I/O.

Thanks…

Hello and welcome @Raghavendra_P

cwltool --target does what you are asking for, it runs a workflow until that target and then stops. You’ll need to provide all of the workflow inputs to use this feature.

cwltool --single-step runs a single workflow step (which might include a scatter or other modifications). The proceeding steps are not run, so you’ll need to provide all the inputs that step needs. Try running without any input object to see what is required; you can also use cwltool --make-template --single-step step_name my_workflow.cwl to get a template input object to fill out.

I hope this helps.

1 Like