def load_snakemake_params():
global is_snakemake_child
if PARAMETER_PASSING_ENVVAR not in os.environ:
return
is_snakemake_child = lambda: True
import json, collections
from snakemake.io import Namedlist
import builtins
options = json.load(open(os.environ[PARAMETER_PASSING_ENVVAR]))
# Unset the parameter file var not to pass to children.
del os.environ[PARAMETER_PASSING_ENVVAR]
for varname, value in options.items():
if not isinstance(value, int):
nl = Namedlist()
for k, v in value:
nl.append(v)
if k is not None:
nl.add_name(k)
value = nl
setattr(builtins, varname, value)
def load_snakemake_params():
global is_snakemake_child
if PARAMETER_PASSING_ENVVAR not in os.environ:
return
is_snakemake_child = lambda: True
import json, collections
from snakemake.io import Namedlist
import builtins
options = json.load(open(os.environ[PARAMETER_PASSING_ENVVAR]))
# Unset the parameter file var not to pass to children.
del os.environ[PARAMETER_PASSING_ENVVAR]
for varname, value in options.items():
if not isinstance(value, int):
nl = Namedlist()
for k, v in value:
nl.append(v)
if k is not None:
nl.add_name(k)
value = nl
setattr(builtins, varname, value)
def recursive_format(ruleinfo):
"""Expand wildcards within ruleinfo
This is not fully implemented!
At this time, only `input` and `output` are expanded within
`params`.
"""
args = {}
for name in ['input', 'output']:
attr = getattr(ruleinfo, name)
if attr is None:
continue
nlist = Namedlist()
for item in flatten(attr[0]):
nlist.append(item)
for key, item in attr[1].items():
nlist.append(item)
nlist.add_name(key)
args[name] = nlist
for key, value in ruleinfo.params[1].items():
if not isinstance(value, str):
continue
value = partial_format(value, **args)
ruleinfo.params[1][key] = value