Ruffus Manual: Table of Contents:

• Ruffus Manual
• Chapter 1 : Arranging tasks into a pipeline with @follows
• Chapter 2: Tasks and Recipes
• Chapter 3: Passing parameters to the pipeline with @files
• Chapter 4: Chaining pipeline Tasks together automatically
• Chapter 5: Tracing pipeline parameters
• Chapter 6: Running Tasks and Jobs in parallel
• Chapter 7: Splitting up large tasks / files with @split
• Chapter 8: Applying the same recipe to create many different files with @transform
• Chapter 9: Merge multiple input into a single result
• Chapter 10: Signal the completion of each stage of our pipeline with @posttask
• Chapter 11: Manage concurrency for a specific task with @jobs_limit
• Chapter 12: Checking dependencies to run tasks in order
• Chapter 13: Generating parameters on the fly with @files
• Chapter 14: @collate: group together disparate input into sets of results
• Chapter 15: add_inputs() and inputs(): Controlling both input and output files with @transform
• Chapter 16: Esoteric: Running jobs in parallel without using files with @parallel
• Chapter 17: Writing custom functions to decide which jobs are up to date
• Chapter 18: Exceptions thrown inside a pipeline
• Chapter 19: Logging progress through a pipeline
• Chapter 20: @files_re: Deprecated syntax using regular expressions