pluto.tools.run_cwl

pluto.tools.run_cwl(testcase, tmpdir, input_json, cwl_file, CWL_ARGS=['--preserve-environment', 'PATH', '--preserve-environment', 'SINGULARITY_CACHEDIR', '--singularity'], print_stdout=False, print_command=False, check_returncode=True, input_json_file=None, debug=False, leave_tmpdir=False, leave_outputs=False, parallel=False, output_dir=None, input_is_file=False)[source]

Run the CWL with cwltool / cwl-runner

Returns

  • dict – output data dictionary loaded from CWL stdout JSON

  • str – path to the output directory from the CWL workflow