add task to nextflow and resume

Question

in test.nf (dsl2) I have

   ... 
   workflow{
       a = Channel...
       processA(a)
       processB(processA.out.emitA)
       processC(processB.out.emitB)
    }

The pipeline completed successfully.

Now I want to add processC_2 that takes the output of processB.

How do I run the workflow to bypass processA execution?

I added processC_2 to test.nf and then did:

nextflow run test.nf -resume run-name

But it doesn't run the newly add process.

How do I achieve my goal?

Thank you!

Answer 1

It is actually very hard to answer this using only the information you have provided. It'd be necessary to actually see your test.nf file and read the processes. The execution seems right and I'd guess that the processB may be not emiting any output as shown in https://www.nextflow.io/docs/latest/process.html#outputs.

It is also possible that when using the -resume together with a specific run-name you may be recovering the state of that specific run as shown here https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html. You can try to execute it without the run-name or without the -resume flag so you can check whether the problem is with the emition and channelling of outputs between processes, or with the -resume flag.