.. include:: ../../global.inc .. include:: manual_chapter_numbers.inc .. _new_manual.table_of_contents: ========================================== Manual ========================================== .. toctree:: :maxdepth: 1 :caption: Manual / Tutorial :name: manual_toc :hidden: introduction.rst transform.rst transform_in_parallel.rst originate.rst pipeline_printout.rst command_line.rst pipeline_printout_graph.rst output_file_names.rst mkdir.rst checkpointing.rst decorators_compendium.rst split.rst merge.rst multiprocessing.rst logging.rst subdivide_collate.rst combinatorics.rst active_if.rst posttask.rst inputs.rst onthefly.rst parallel.rst check_if_uptodate.rst flowchart_colours.rst dependencies.rst exceptions.rst list_of_ruffus_names.rst deprecated_files.rst deprecated_files_re.rst #################################################################### **Ruffus** Manual Table of Contents #################################################################### Download as :download:`pdf <../../static_data/ruffus.pdf>`. * |new_manual.introduction.chapter_num|: :ref:`An introduction to basic Ruffus syntax ` * |new_manual.transform.chapter_num|: :ref:`Transforming data in a pipeline with @transform ` * |new_manual.transform_in_parallel.chapter_num|: :ref:`More on @transform-ing data ` * |new_manual.originate.chapter_num|: :ref:`Creating files with @originate ` * |new_manual.pipeline_printout.chapter_num|: :ref:`Understanding how your pipeline works with pipeline_printout() ` * |new_manual.cmdline.chapter_num|: :ref:`Running Ruffus from the command line with ruffus.cmdline ` * |new_manual.pipeline_printout_graph.chapter_num|: :ref:`Displaying the pipeline visually with pipeline_printout_graph() ` * |new_manual.output_file_names.chapter_num|: :ref:`Specifying output file names with formatter() and regex() ` * |new_manual.mkdir.chapter_num|: :ref:`Preparing directories for output with @mkdir ` * |new_manual.checkpointing.chapter_num|: :ref:`Checkpointing: Interrupted Pipelines and Exceptions ` * |new_manual.decorators_compendium.chapter_num|: :ref:`Pipeline topologies and a compendium of Ruffus decorators ` * |new_manual.split.chapter_num|: :ref:`Splitting up large tasks / files with @split ` * |new_manual.merge.chapter_num|: :ref:`@merge multiple input into a single result ` * |new_manual.logging.chapter_num|: :ref:`Logging progress through a pipeline ` * |new_manual.multiprocessing.chapter_num|: :ref:`Multiprocessing, drmaa and Computation Clusters ` * |new_manual.subdivide_collate.chapter_num|: :ref:`@subdivide tasks to run efficiently and regroup with @collate ` * |new_manual.combinatorics.chapter_num|: :ref:`@combinations, @permutations and all versus all @product ` * |new_manual.active_if.chapter_num|: :ref:`Turning parts of the pipeline on and off at runtime with @active_if ` * |new_manual.inputs.chapter_num|: :ref:`Manipulating task inputs via string substitution with inputs() and add_inputs() ` * |new_manual.posttask.chapter_num|: :ref:`Signal the completion of each stage of our pipeline with @posttask ` * |new_manual.on_the_fly.chapter_num|: :ref:`Esoteric: Generating parameters on the fly with @files ` * |new_manual.parallel.chapter_num|: :ref:`Esoteric: Running jobs in parallel without files using @parallel ` * |new_manual.check_if_uptodate.chapter_num|: :ref:`Esoteric: Writing custom functions to decide which jobs are up to date with @check_if_uptodate ` * |new_manual.flowchart_colours.chapter_num| :ref:`Flow Chart Colours with pipeline_printout_graph ` * |new_manual.dependencies.chapter_num| :ref:`Under the hood: How dependency works ` * |new_manual.exceptions.chapter_num| :ref:`Exceptions thrown inside pipelines ` * |new_manual.ruffus_names.chapter_num| :ref:`Names (keywords) exported from Ruffus ` * |new_manual.deprecated_files.chapter_num|: :ref:`Legacy and deprecated syntax @files ` * |new_manual.deprecated_files_re.chapter_num|: :ref:`Legacy and deprecated syntax @files_re ` **Ruffus** Manual: List of Example Code for Each Chapter: * :ref:`new_manual.introduction.code` * :ref:`new_manual.transform.code` * :ref:`new_manual.transform_in_parallel.code` * :ref:`new_manual.originate.code` * :ref:`new_manual.pipeline_printout.code` * :ref:`new_manual.pipeline_printout_graph.code` * :ref:`new_manual.output_file_names.code` * :ref:`new_manual.mkdir.code` * :ref:`new_manual.checkpointing.code` * :ref:`new_manual.split.code` * :ref:`new_manual.merge.code` * :ref:`new_manual.multiprocessing.code` * :ref:`new_manual.logging.code` * :ref:`new_manual.subdivide_collate.code` * :ref:`new_manual.combinatorics.code` * :ref:`new_manual.inputs.code` * :ref:`new_manual.on_the_fly.code` .. toctree:: :caption: Example code :name: example_code_toc :hidden: :maxdepth: 1 introduction_code.rst transform_code.rst transform_in_parallel_code.rst originate_code.rst pipeline_printout_code.rst pipeline_printout_graph_code.rst output_file_names_code.rst mkdir_code.rst checkpointing_code.rst split_code.rst merge_code.rst multiprocessing_code.rst logging_code.rst subdivide_collate_code.rst combinatorics_code.rst inputs_code.rst onthefly_code.rst flowchart_colours_code.rst .. toctree:: :maxdepth: 2 :hidden: ../../examples/bioinformatics/index.rst ../../examples/bioinformatics/part2.rst ../../examples/bioinformatics/part1_code.rst ../../examples/bioinformatics/part2_code.rst ../../examples/paired_end_data.py.rst