advanced lesson: inplace editing of existing files

[mr-c]

This lesson needs to make very clear that only some CWL engines support this extension, but that it is planned for CWL v1.1

Known implementors:

• cwlref-runner
• arvados

Need to check

• [ ] toil-cwl-runner
• [ ] rabix executor

Use case: "ms" measurement sets from radio astronomy (essentially they are very large (terabyte) databases spread across many files in a directory)

If you need to manipulate a dataset but don't care if it is copied use:

requirements:
  InitialWorkDirRequirement:
    listing:
      - entry: $(inputs.dataset)
        writable: true

inputs:
  dataset: Directory

If you do care about not copying (manipulate in place):

requirements:
  InitialWorkDirRequirement:
    listing:
      - entry: $(inputs.dataset)
        writable: true
  cwltool:InplaceUpdateRequirement:
    inplaceUpdate: true

inputs:
  dataset: Directory

$namespaces:
  cwltool: "http://commonwl.org/cwltool#"