Chapter 4: Creating files with @originate


Remember to look at the example code:

Simplifying our example with @originate

Our previous pipeline example started off with a set of files which we had to create first.

This is a common task: pipelines have to start somewhere.

Ideally, though, we would only want to create these starting files if they didn’t already exist. In other words, we want a sort of @transform which makes files from nothing (None?).

This is exactly what @originate helps you to do.

Rewriting our pipeline with @originate gives the following three steps:

from ruffus import *

#   create initial files
@originate([   ['job1.a.start', 'job1.b.start'],
               ['job2.a.start', 'job2.b.start'],
               ['job3.a.start', 'job3.b.start']    ])
def create_initial_file_pairs(output_files):
    # create both files as necessary
    for output_file in output_files:
        with open(output_file, "w") as oo: pass

#   first task
@transform(create_initial_file_pairs, suffix(".start"), ".output.1")
def first_task(input_files, output_file):
    with open(output_file, "w"): pass

#   second task
@transform(first_task, suffix(".output.1"), ".output.2")
def second_task(input_files, output_file):
    with open(output_file, "w"): pass

#       Run
    Job  = [None -> [job1.a.start, job1.b.start]] completed
    Job  = [None -> [job2.a.start, job2.b.start]] completed
    Job  = [None -> [job3.a.start, job3.b.start]] completed
Completed Task = create_initial_file_pairs
    Job  = [[job1.a.start, job1.b.start] -> job1.a.output.1] completed
    Job  = [[job2.a.start, job2.b.start] -> job2.a.output.1] completed
    Job  = [[job3.a.start, job3.b.start] -> job3.a.output.1] completed
Completed Task = first_task
    Job  = [job1.a.output.1 -> job1.a.output.2] completed
    Job  = [job2.a.output.1 -> job2.a.output.2] completed
    Job  = [job3.a.output.1 -> job3.a.output.2] completed
Completed Task = second_task