ruffus cmdline and OO syntax

[mbiokyle29]

Hello!

New object oriented syntax is awesome. I was wondering if we could get updates to the docs for working with the new pipeline syntax and the ruffus cmdline approach.

What I mean:

# new syntax
pipeline = Pipeline()

# build pipeline

pipeline.run()

With cmdline

import ruffus.cmdline as cmdline
parser = cmdline.get_argparse(description='WHAT DOES THIS PIPELINE DO?')
#  cmd ops
options = parser.parse_args()

#  pipelined functions go here
cmdline.run (options)

How should we make cmdline and the pipeline object work together? I tried a few different ways (running one or the other, passing pipeline to cmd, etc) but nothing seemed to work correctly.

[Jerry-Ma]

If you only have one Pipeline object, then cmdline.run(options) will run that pipeline.