adrabent

cwltool: Input of type Directory[] stays readonly if using writable: true in InitialWorkDirRequirement

3

Dear cwltool developers. ## Expected Behavior I created a CWL step that takes an input of type `Directory[]`. This step should be able to read-write on the input data. ```...

cwltool: Step using InplaceUpdate conflicts with still active readers from an already finished job

8

## Expected Behavior cwltool should pass and not through an error ## Actual Behavior cwltool throws an error ## Workflow Code ``` class: Workflow cwlVersion: v1.2 id: minimal_example label: minimal_example...

toil ignores LoadListingRequirement

5

When using `toil-cwl-runner` it seems like it always uses `deep_listing` when files or directories are mounted for running within Docker or Singularity. If I try to add [LoadListingRequirement](https://www.commonwl.org/v1.2/CommandLineTool.html#LoadListingRequirement) and set...

--- ## Expected Behavior cwltool should treat the input type identical to the output type (at least if it accepts two different types) ## Actual Behavior cwltool crashes, because it...

cwltool throws validation errors despite consistent type declarations

1

--- ## Expected Behavior `cwltool --validate` should not show any warnings ## Actual Behavior cwltool throws a workflow checker warning, although all types are chosen consistently. The warning output complain...