.. include:: global.inc *************************** **Ruffus** documentation *************************** ===================== Start Here: ===================== .. toctree:: :maxdepth: 1 installation.rst tutorials/simple_tutorial/simple_tutorial.rst Manual ===================== Overview: ===================== .. toctree:: :maxdepth: 2 cheatsheet.rst pipeline_functions.rst installation.rst design.rst Bugs and Updates Future plans faq.rst glossary.rst gallery.rst examples/code_template/code_template.rst ===================== Examples ===================== .. toctree:: :maxdepth: 2 examples/bioinformatics/index.rst examples/bioinformatics/part2.rst examples/bioinformatics/part1_code.rst examples/bioinformatics/part2_code.rst examples/colour_schemes/flowchart_colours.rst examples/colour_schemes/flowchart_colours_code.rst examples/code_template/code_template_code.rst tutorials/manual/manual_code.rst tutorials/simple_tutorial/simple_tutorial_code.rst ===================== Reference: ===================== ###################### Decorators ###################### .. toctree:: :maxdepth: 1 decorators/decorators.rst decorators/indicator_objects.rst .. topic:: Basic .. toctree:: :maxdepth: 1 decorators/follows.rst decorators/files.rst .. topic:: Core .. toctree:: :maxdepth: 1 decorators/split.rst decorators/transform.rst decorators/merge.rst decorators/posttask.rst .. topic:: For advanced users .. toctree:: :maxdepth: 1 decorators/jobs_limit.rst decorators/split_ex.rst decorators/transform_ex.rst decorators/collate.rst decorators/collate_ex.rst .. topic:: Esoteric .. toctree:: :maxdepth: 1 decorators/files_ex.rst decorators/parallel.rst decorators/check_if_uptodate.rst decorators/files_re.rst ###################### Modules: ###################### .. toctree:: :maxdepth: 2 task.rst proxy_logger.rst .. comment graph.rst print_dependencies.rst adjacent_pairs_iterate.rst ===================== Indices and tables ===================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`