Separate GWF workflows for each population

workflows_per_population.py

from gwf import Workflow, AnonymousTarget

def mask_template(path):
    inputs = {'path': path}
    outputs = {'path': path + '.masked'}
    options = {}
    spec = """./some_command {}""".format(path)
    return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)

def step_one_template(path):
    inputs = {'path': path}
    outputs = {'path': path + '.first'}
    options = {}
    spec = """./some_command {}""".format(path)
    return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)

def step_two_template(path):
    inputs = {'path': path}
    outputs = {'path': path + '.second'}
    options = {}
    spec = """./some_command {}""".format(path)
    return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)

input_files = {'CEU': ['ceu_chr1.txt', 'ceu_chr2.txt'],
               'CHB': ['chb_chr1.txt', 'chb_chr2.txt'],
}

for pop, paths in input_files.items():
    workflow_name = pop
    wf = Workflow(name=workflow_name)
    globals()[workflow_name] = wf

    step_one_tasks = wf.map(step_one_template, paths)
    step_two_tasks = wf.map(step_two_template, step_one_tasks.outputs)

# The advantage/drawback is that you need to run each workflow separately like this:
# gwf -f workflow.py:CEU run