def prep_variant_cwl(samples, out_dir, out_file):
"""Output a CWL decription for running a variant calling workflow.
"""
step_dir = utils.safe_makedir(os.path.join(out_dir, "steps"))
sample_json, variables = _flatten_samples(samples, out_file)
out = _cwl_workflow_template(variables)
parent_wfs = []
for cur in workflow.variant(variables):
if cur[0] == "step":
_, name, parallel, inputs, outputs = cur
step_file = _write_tool(step_dir, name, inputs, outputs, parallel)
out["steps"].append(_step_template(name, step_file, inputs, outputs, parallel))
elif cur[0] == "upload":
out["outputs"] = cur[1]
elif cur[0] == "wf_start":
parent_wfs.append(out)
out = _cwl_workflow_template(cur[1])
elif cur[0] == "wf_finish":
_, name, parallel, inputs, outputs = cur
wf_out_file = "wf-%s.cwl" % name
with open(os.path.join(out_dir, wf_out_file), "w") as out_handle:
yaml.safe_dump(out, out_handle, default_flow_style=False, allow_unicode=False)
out = parent_wfs.pop(-1)
out["steps"].append(_step_template(name, wf_out_file, inputs, outputs, parallel))
else:
raise ValueError("Unexpected workflow value %s" % str(cur))
with open(out_file, "w") as out_handle:
yaml.safe_dump(out, out_handle, default_flow_style=False, allow_unicode=False)
return out_file, sample_json
def prep_variant_cwl(samples, out_dir, out_file):
"""Output a CWL decription for running a variant calling workflow.
"""
step_dir = utils.safe_makedir(os.path.join(out_dir, "steps"))
sample_json, variables = _flatten_samples(samples, out_file)
out = _standard_bcbio_cwl(samples, variables)
out["steps"] = []
for name, inputs, outputs in workflow.variant(variables):
out["steps"].append(_step_template(name, step_dir, inputs, outputs))
with open(out_file, "w") as out_handle:
yaml.safe_dump(out,
out_handle,
default_flow_style=False,
allow_unicode=False)
return out_file, sample_json
def prep_variant_cwl(samples, out_dir, out_file):
"""Output a CWL decription for running a variant calling workflow.
"""
step_dir = utils.safe_makedir(os.path.join(out_dir, "steps"))
sample_json, variables = _flatten_samples(samples, out_file)
out = _standard_bcbio_cwl(samples, variables)
out["steps"] = []
for name, parallel, inputs, outputs in workflow.variant(variables):
if name == "upload":
out["outputs"] = outputs
else:
out["steps"].append(_step_template(name, step_dir, inputs, outputs, parallel))
with open(out_file, "w") as out_handle:
yaml.safe_dump(out, out_handle, default_flow_style=False, allow_unicode=False)
return out_file, sample_json