Input variable values

As we've seen in the Accessing files section, step input files are created from either a from-workflow or from-step declaration. How does the step deal with Project files (which are file-links) and step files (which are directory-links)?

The answer is - they don't know the difference. The workflow engine ensures this by prefixing the filename with an instance sub-directory when the step is using a file from a prior step. Let's look at two variable values in a step that uses a Project file and a prior step file using the following workflow excerpt: -

- name: step-3
  plumbing:
  - variable: inputFile
    from-workflow:
      variable: candidateMolecules
  - variable: propertyFile
    from-step:
      name: step-2
      variable: outputFile

For the sake of this example, to help illustrate how the engine sets the values of step-3's variables, let's also assume the values of the candidateMolecules variable is the name of a Project file called molecules.smi and step-2's outputFile is properties.txt (a file in its own instance directory). Let's also assume step-2's instance directory is called .instance-123435678.

In this scenario the workflow engine will launch step-3 with the following variables and values: -

{
  "inputFile": "molecules.smi",
  "propertyFile": ".instance-123435678/properties.txt"
}

The DM will hard-link the file molecules.smi and the instance directory .instance-123435678 into step-3's own instance directory.

Special considerations for "combining" steps