def _step_template(name, run_file, inputs, outputs, parallel, step_parallelism, scatter=None):
"""Templating function for writing a step to avoid repeating namespaces.
"""
scatter_inputs = []
sinputs = []
for inp in inputs:
step_inp = {"id": workflow.get_base_id(inp["id"]), "source": inp["id"]}
if inp.get("wf_duplicate"):
step_inp["id"] += "_toolinput"
for attr in ["source", "valueFrom"]:
if attr in inp:
step_inp[attr] = inp[attr]
sinputs.append(step_inp)
# An initial parallel scatter and multiple chained parallel sample scatters
if (parallel == "multi-parallel" and
(not step_parallelism or
step_parallelism.get(workflow.get_step_prefix(inp["id"])) == "multi-parallel")):
scatter_inputs.append(step_inp["id"])
# scatter on inputs from previous processes that have been arrayed
elif (_is_scatter_parallel(parallel) and (_do_scatter_var(inp, parallel)
or (scatter and inp["id"] in scatter))):
scatter_inputs.append(step_inp["id"])
out = {"run": run_file,
"id": name,
"in": sinputs,
"out": [{"id": workflow.get_base_id(output["id"])} for output in outputs]}
if _is_scatter_parallel(parallel):
assert scatter_inputs, "Did not find items to scatter on: %s" % name
out.update({"scatterMethod": "dotproduct",
"scatter": scatter_inputs})
return out
def _step_template(name, run_file, inputs, outputs, parallel, step_parallelism, scatter=None):
"""Templating function for writing a step to avoid repeating namespaces.
"""
scatter_inputs = []
sinputs = []
for inp in inputs:
step_inp = {"id": workflow.get_base_id(inp["id"]), "source": inp["id"]}
if inp.get("wf_duplicate"):
step_inp["id"] += "_toolinput"
for attr in ["source", "valueFrom"]:
if attr in inp:
step_inp[attr] = inp[attr]
sinputs.append(step_inp)
# An initial parallel scatter and multiple chained parallel sample scatters
if (parallel == "multi-parallel" and
(not step_parallelism or
step_parallelism.get(workflow.get_step_prefix(inp["id"])) == "multi-parallel")):
scatter_inputs.append(step_inp["id"])
# scatter on inputs from previous processes that have been arrayed
elif (_is_scatter_parallel(parallel) and (_do_scatter_var(inp, parallel)
or (scatter and inp["id"] in scatter))):
scatter_inputs.append(step_inp["id"])
out = {"run": run_file,
"id": name,
"in": sinputs,
"out": [{"id": workflow.get_base_id(output["id"])} for output in outputs]}
if _is_scatter_parallel(parallel):
assert scatter_inputs, "Did not find items to scatter on: %s" % name
out.update({"scatterMethod": "dotproduct",
"scatter": scatter_inputs})
return out