[cwl workflow steps] explicit I/O relationship, workflow

Question

[billy0210828]

link: https://github.com/common-workflow-language/common-workflow-language/issues/841

Hi everyone, Link: https://github.com/r06942072/CWL_Common-Workflow-Language/blob/dev/final-workflow.cwl I met some problems when using CWL workflow

I know that the steps order is decided by input/output relationship, so I fed out_tree in setup_tree to in_dir in copy2data.

However, I wonder if there is a way to explicitly specify the order of workflow. Like Step1. setup_tree Step2. download_genomic ........

Thank you

Best, Chun-Hung

Answer 1

[kaushik.ghose]

As mentioned in that issue:

CWL is declarative in nature, so you can't directly control these steps (and should not have to, like in functional programming).

The reason why you have an order of operations is because there is a dependency, perhaps hidden, in those steps. In CWL, like in functional paradigms, these dependencies should naturally come out of the way the steps are connected. If there is no connection from A to B, then B does not depend on A and it does not need to start after A.