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sr.c – Running with StreamFlow

StreamFlow has a different command-line interface than cwltool or Toil. This directory contains a wrapper script, streamflow-run-wrapper.sh that creates the StreamFlow input file and runs the workflow.

This is an example StreamFlow input file:

version: v1.0
workflows:
  workflow_name:
    type: cwl
    config:
      file: "/home/kinow/Development/python/workspace/cwl-mpi/workflows/mpich-sr/mpirun-base-command.cwl"
      docker:
        - step: /
          deployment:
            type: singularity
            config: {}

The wrapper script, streamflow-run-wrapper.sh takes a mandatory argument, the path to the StreamFlow input file. A second optional argument is the path to the job file. Another optional argument is the flag --singularity, which adds the docker: YAML section above.

The Makefile build script can be used to run the tests with StreamFlow by setting the CWL_RUNNER variable to streamflow-run-wrapper.sh.

Example usage:

$ make CWL_RUNNER=./streamflow-run-wrapper.sh mpicc
$ make CWL_RUNNER=./streamflow-run-wrapper.sh DEBUG=1 mpirun-base  # this adds --debug