This repo demonstrates an issue or misunderstanding with nextflow workflows.

The workflow in main.nf runs an imported workflow three times, with inputs inputs/a, inputs/b, and inputs/c

Each instance of the workflow is applied to a single input, i.e. inputs/a. I would expect each process called by foo to be given the same input (since that is exactly how it is defined in the workflow). However when p3 executes, taking p1.out and p2.out as inputs, it receives inputs from different instances of the foo workflow.

I.e. one instance of foo is given inputs/a, but calls p3 with some random combination of inputs/a, inputs/b, and inputs/c.

The instance of foo called with inputs/a as input should never have access to the files inputs/b or inputs/c

To see it in action, run nextflow run main.nf multiple times and check the contents of the workdir for p3. The subdirs output_p3/output_p1 and output_p3/output_p2 should both contain the same file - a, b or c. Instead there is a random combination that changes each time nextflow runs.