Use an environment variable as the default resources tmpdir in a snakemake workflow

tmpdir_envvar.smk

# For a local instance, use --default_resources 'tmpdir="$MYENV_VAR"'
# Everything should work properly

# For a cluster scheduling instance, use --default_resources 'tmpdir="$$MYENV_VAR"'
# The double dollar sign is needed for escaping. 
# Note that you won't be able to use this tmpdir on localrules (only a concern in cluster mode)

# The `tmpdir` variable becomes available for use throughout the workflow

def eval_environ(s):
    s = s.strip("'\"") if s else s
    if s and len(s) > 1 and s[0] == "$":
        if s[1] == "$":
            return s[1:]
        return os.environ.get(s[1:])
    return s

tmpdir = eval_environ(workflow.default_resources._args.get("tmpdir"))

if tmpdir is not None:
    workflow.default_resources.set_resource("tmpdir", tmpdir)