Separate GWF workflows for two similar analyses

workflows_per_analysis.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'],
}

workflow_name = 'no.masking'
wf = Workflow(name=workflow_name)
globals()[workflow_name] = wf
for pop, paths in input_files.items():
    step_one_tasks = wf.map(step_one_template, paths, name=f"step_one_{pop}")
    step_two_tasks = wf.map(step_two_template, step_one_tasks.outputs, name=f"step_two_{pop}")

workflow_name = 'repeat.masking'
wf = Workflow(name=workflow_name)
globals()[workflow_name] = wf
for pop, paths in input_files.items():
    mask_tasks = wf.map(mask_template, paths, name=f"mask_{pop}")
    step_one_tasks = wf.map(step_one_template, mask_tasks.outputs, name=f"step_one_{pop}")
    step_two_tasks = wf.map(step_two_template, step_one_tasks.outputs, name=f"step_two_{pop}")