Closed biokcb closed 6 years ago
This is a bug, when using a subflow name as a reference, see e0072bf
The -w and -o should use absolute path, e.g.
cwlexec -X -pe PATH -w workdir -o outdir two_input_workflow.cwl inp.yml > 2inp.out
should be
cwlexec -X -pe PATH -w $(pwd)/workdir -o $(pwd)/outdir two_input_workflow.cwl inp.yml > 2inp.out
Hi,
We have a workflow which has two steps. Each step calls a subworkflow that calls a command line tool. When the steps/subworkflows are independent of each other the run succeeds (
two_input_workflow.cwl
), but when one step relies on output of another step (one_input_workflow.cwl
) it fails to resolve the workflow, giving the following error:The full output (
1inp.out
) is attached along with both the failure and success example. This seems to happen with just subworkflows as far as we can tell.SubworkflowDependenciesError.tar.gz