fix: check template rendering output for leaked input file paths

docs/snakefiles/rules.rst

@@ -2712,7 +2712,7 @@ Apart from Jinja2, Snakemake supports `YTE <https://github.com/koesterlab/yte>`_
 
 .. code-block:: python
 
-    rule render_jinja2_template:
+    rule render_yte_template:
         input:
             "some-yte-template.yaml"
         output:
@@ -2737,7 +2737,33 @@ Analogously to the jinja2 case YTE has access to ``params``, ``wildcards``, and
         - b
         - ?config["threshold"]
 
-Template rendering rules are always executed locally, without submission to cluster or cloud processes (since templating is usually not resource intensive).
+By default, template rendering rules are executed locally, without submission to cluster or cloud processes (since templating is usually not resource intensive).
+However, if a :ref:`storage plugin <storage-support>` is used, a template rule can theoretically leak paths to local copies of the storage files into the rendered template.
+This can happen if the template inserts the path of an input file into the rendered output.
+Snakemake tries to detect such cases by checking the template output.
+To avoid such leaks (only required if your template does something like that with an input file path), you can assign the same :ref:`group <job_grouping>` to your template rule and the consuming rule, and in addition mark the template output as ``temp()``, i.e.:
+
+.. code-block:: python
+
+    rule render_yte_template:
+        input:
+            "some-yte-template.yaml"
+        output:
+            temp("results/{sample}.rendered-version.yaml")
+        params:
+            foo=0.1
+        group: "some-group"
+        template_engine:
+            "yte"
+
+    rule consume_template:
+        input:
+            "results/{sample}.rendered-version.yaml"
+        output:
+            "results/some-output.txt"
+        group: "some-group"
+        shell:
+            "sometool {input} {output}"
 
 .. _snakefiles_mpi_support:
 

snakemake/jobs.py

@@ -18,6 +18,7 @@
 from abc import ABC, abstractmethod
 from snakemake.settings import DeploymentMethod
 
+from snakemake.template_rendering import check_template_output
 from snakemake_interface_common.utils import lazy_property
 from snakemake_interface_executor_plugins.jobs import (
     JobExecutorInterface,
@@ -1101,6 +1102,15 @@ async def postprocess(
                     wait_for_local=True,
                 )
             self.dag.unshadow_output(self, only_log=error)
+
+            if (
+                not error
+                and self.rule.is_template_engine
+                and not is_flagged(self.output[0], "temp")
+            ):
+                # TODO also check if consumers are executed on the same node
+                check_template_output(self)
+
             await self.dag.handle_storage(
                 self, store_in_storage=store_in_storage, store_only_log=error
             )

snakemake/template_rendering/__init__.py

@@ -57,3 +57,17 @@ def render_template(engine, input, output, params, wildcards, config, rule):
             )
     except Exception as e:
         raise WorkflowError(f"Error rendering template in rule {rule}.", e)
+
+
+def check_template_output(job):
+    with open(job.output[0]) as out:
+        for l in out:
+            for f in job.input:
+                if f.is_storage and f in l:
+                    raise WorkflowError(
+                        "Output of template_engine rule contains local path to input file "
+                        f"from storage: {f} for {f.storage_object.query}. "
+                        "However, this path is variable as it can change between runs (e.g. when "
+                        "the storage local prefix is modified). To circumvent this issue, place the "
+                        "rule in one group with the consumer(s) and mark the output as temp()."
+                    )