├── .codacy.yml ├── .editorconfig ├── .gitignore ├── .travis.yml ├── .zenodo.json ├── CHANGELOG.md ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.rst ├── codemeta.json ├── docs ├── Makefile ├── _templates │ └── sidebarintro.html ├── adding_outputs.rst ├── adding_workflow_steps.rst ├── conf.py ├── cwl_tips_tricks.rst ├── enable_logging.rst ├── examples.rst ├── images │ ├── add-multiply-example-workflow.png │ └── nlppln-anonymize-workflow.png ├── index.rst ├── installation.rst ├── listing_steps.rst ├── loading_steps.rst ├── make.bat ├── nlppln_anonymize.rst ├── printing_workflows.rst ├── saving_workflows.rst ├── setting_documentation.rst ├── useful_tools.rst ├── user_manual.rst └── workflow_inputs.rst ├── requirements.txt ├── scriptcwl ├── __init__.py ├── examples │ ├── __init__.py │ ├── add.cwl │ ├── add.py │ ├── add_multiply_example.cwl │ ├── multiply.cwl │ └── multiply.py ├── library.py ├── reference.py ├── scriptcwl.py ├── step.py ├── workflow.py └── yamlutils.py ├── setup.cfg ├── setup.py └── tests ├── data ├── echo-no-shebang.cwl ├── echo-wc.workflowstep.cwl ├── echo.scattered.cwl ├── file-names │ ├── echo-with-minuses.cwl │ ├── echo-with-minuses_and_underscores.cwl │ ├── echo_with_minuses-and-underscores.cwl │ └── echo_with_underscores.cwl ├── misc │ ├── align-dir-pack.cwl │ ├── echo2.cwl │ ├── echo3.cwl │ └── non-python-names.cwl ├── tools │ ├── echo.cwl │ ├── multiple-out-args.cwl │ └── wc.cwl └── workflows │ ├── echo-wc.cwl │ ├── echo-wc_inline.cwl │ └── echo-wc_wd.cwl ├── test_library.py ├── test_lint.py ├── test_scriptcwl.py ├── test_step.py ├── test_workflow.py └── test_yamlutils.py /.codacy.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NLeSC/scriptcwl/HEAD/.codacy.yml -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- 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