Manual¶

Ruffus Manual Table of Contents¶

Download as pdf.

• Chapter 1: An introduction to basic Ruffus syntax
• Chapter 2: Transforming data in a pipeline with @transform
• Chapter 3: More on @transform-ing data
• Chapter 4: Creating files with @originate
• Chapter 5: Understanding how your pipeline works with pipeline_printout()
• Chapter 6: Running Ruffus from the command line with ruffus.cmdline
• Chapter 7: Displaying the pipeline visually with pipeline_printout_graph()
• Chapter 8: Specifying output file names with formatter() and regex()
• Chapter 9: Preparing directories for output with @mkdir
• Chapter 10: Checkpointing: Interrupted Pipelines and Exceptions
• Chapter 11: Pipeline topologies and a compendium of Ruffus decorators
• Chapter 12: Splitting up large tasks / files with @split
• Chapter 13: @merge multiple input into a single result
• Chapter 15: Logging progress through a pipeline
• Chapter 14: Multiprocessing, drmaa and Computation Clusters
• Chapter 16: @subdivide tasks to run efficiently and regroup with @collate
• Chapter 17: @combinations, @permutations and all versus all @product
• Chapter 18: Turning parts of the pipeline on and off at runtime with @active_if
• Chapter 20: Manipulating task inputs via string substitution with inputs() and add_inputs()
• Chapter 19: Signal the completion of each stage of our pipeline with @posttask
• Chapter 21: Esoteric: Generating parameters on the fly with @files
• Chapter 22: Esoteric: Running jobs in parallel without files using @parallel
• Chapter 23: Esoteric: Writing custom functions to decide which jobs are up to date with @check_if_uptodate
• Appendix 1 Flow Chart Colours with pipeline_printout_graph
• Appendix 2 Under the hood: How dependency works
• Appendix 3 Exceptions thrown inside pipelines
• Appendix 4 Names (keywords) exported from Ruffus
• Appendix 5: Legacy and deprecated syntax @files
• Appendix 6: Legacy and deprecated syntax @files_re

Ruffus Manual: List of Example Code for Each Chapter:

• Chapter 1: Python Code for An introduction to basic Ruffus syntax
• Chapter 1: Python Code for Transforming data in a pipeline with @transform
• Chapter 3: Python Code for More on @transform-ing data
• Chapter 4: Python Code for Creating files with @originate
• Chapter 5: Python Code for Understanding how your pipeline works with pipeline_printout(...)
• Chapter 7: Python Code for Displaying the pipeline visually with pipeline_printout_graph(...)
• Chapter 8: Python Code for Specifying output file names with formatter() and regex()
• Chapter 9: Python Code for Preparing directories for output with @mkdir()
• Chapter 10: Python Code for Checkpointing: Interrupted Pipelines and Exceptions
• Chapter 12: Python Code for Splitting up large tasks / files with @split
• Chapter 13: Python Code for @merge multiple input into a single result
• Chapter 14: Python Code for Multiprocessing, drmaa and Computation Clusters
• Chapter 15: Python Code for Logging progress through a pipeline
• Chapter 16: Python Code for @subdivide tasks to run efficiently and regroup with @collate
• Chapter 17: Python Code for @combinations, @permutations and all versus all @product
• Chapter 20: Python Code for Manipulating task inputs via string substitution using inputs() and add_inputs()
• Chapter 21: Esoteric: Python Code for Generating parameters on the fly with @files