Provide wrapper functors to allow re-use of the same function in ruffus

[AndreasHeger]

Ruffus does not permit to use the same function twice in the same workflow. This can be annoying as you might have files of the same type produced in the workflow at different stages, but want to run the same QC function on them.

The following pattern is a start:

class EmptyRunner(object):

    def __init__(self, name):
        self.__name__ = name

    def __call__(self, *args, **kwargs):
        pass


class PassThroughRunner(object):
    def __init__(self, name, f):
        self.__name__ = name
        self.f = f

    def __call__(self, *args, **kwargs):
        self.f(*args, **kwargs)

Usage:

def my_qc_fun(infile, outfile):
    pass

task_qc_a = pipeline.merge(
        task_func=PassThroughRunner(
            name="run_qc_1",
            f=my_qc_function),
        input=task_build_data1,
        output="a.qc")

task_qc_b = pipeline.merge(
        task_func=PassThroughRunner(
            name="run_qc_2",
            f=my_qc_function),
        input=task_build_data1,
        output="b.qc")

Note how my_qc_function is reused.

Also:

task_all = pipeline.merge(
        task_func=EmptyRunner(name="all"),
        input=[task_plot_tests],
        output="all")

which allows you to run make all

[AndreasHeger]

See pipeline/wrappers.py , 70567d3