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March 20, 2020 14:42
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Manual naming reused GWF templates
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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'], | |
} | |
gwf = Workflow() | |
for pop, paths in input_files.items(): | |
step_one_tasks = gwf.map(step_one_template, paths, name=f"no_repeats_step_one_{pop}") | |
step_two_tasks = gwf.map(step_two_template, step_one_tasks.outputs, name=f"no_repeats_step_two_{pop}") | |
for pop, paths in input_files.items(): | |
mask_tasks = gwf.map(mask_template, paths, name=f"with_repeats_{pop}") | |
step_one_tasks = gwf.map(step_one_template, mask_tasks.outputs, name=f"with_repeats_step_one_{pop}") | |
step_two_tasks = gwf.map(step_two_template, step_one_tasks.outputs, name=f"with_repeats_step_two_{pop}") |
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