fix: support multiple input files for template_engine rules

docs/snakefiles/rules.rst

@@ -2009,10 +2009,24 @@ Consider the following example:
             "jinja2"
 
 Here, Snakemake will automatically use the specified template engine `Jinja2 <https://jinja.palletsprojects.com/>`_ to render the template given as input file into the given output file.
-Template rendering rules may only have a single input and output file.
 The template_engine instruction has to be specified at the end of the rule.
+Template rendering rules may only have a single output file.
+If the rule needs more than one input file, there has to be one input file called ``template``, pointing to the main template to be used for the rendering:
 
-The template itself has access to ``params``, ``wildcards``, and ``config``,
+.. code-block:: python
+
+    rule render_jinja2_template:
+        input:
+            template="some-jinja2-template.txt",
+            other_file="some-other-input-file-used-by-the-template.txt"
+        output:
+            "results/{sample}.rendered-version.txt"
+        params:
+            foo=0.1
+        template_engine:
+            "jinja2"
+
+The template itself has access to ``input``, ``params``, ``wildcards``, and ``config``,
 which are the same objects you can use for example in the ``shell`` or ``run`` directive, 
 and the same objects as can be accessed from ``script`` or ``notebook`` directives (but in the latter two cases they are stored behind the ``snakemake`` object which serves as a dedicated namespace to avoid name clashes).
 

snakemake/parser.py

@@ -654,7 +654,7 @@ class TemplateEngine(Script):
     end_func = "render_template"
 
     def args(self):
-        yield (", input, output, params, wildcards, config")
+        yield (", input, output, params, wildcards, config, rule")
 
 
 class CWL(Script):

snakemake/report/__init__.py

@@ -473,7 +473,7 @@ def render(self, env, rst_links, categories, files):
                 job.threads,
                 job.resources,
                 job.log,
-                job.dag.workflow.config,
+                job.rule.module_globals["config"],
                 job.rule.name,
                 None,
             )

snakemake/rules.py

@@ -124,6 +124,7 @@ def __init__(self, *args, lineno=None, snakefile=None, restart_times=0):
             self.log_modifier = None
             self.benchmark_modifier = None
             self.ruleinfo = None
+            self.module_globals = None
         elif len(args) == 1:
             other = args[0]
             self.name = other.name
@@ -177,6 +178,7 @@ def __init__(self, *args, lineno=None, snakefile=None, restart_times=0):
             self.log_modifier = other.log_modifier
             self.benchmark_modifier = other.benchmark_modifier
             self.ruleinfo = other.ruleinfo
+            self.module_globals = other.module_globals
 
     def dynamic_branch(self, wildcards, input=True):
         def get_io(rule):

snakemake/template_rendering/__init__.py

@@ -1,12 +1,26 @@
 from abc import ABC, abstractmethod
 
+from snakemake.exceptions import WorkflowError
+
 
 class TemplateRenderer(ABC):
     def __init__(self, input, output, params, wildcards, config):
-        assert len(input) == 1
-        assert len(output) == 1
-
-        self.input_file = input[0]
+        if len(output) != 1:
+            raise ValueError(
+                "More than one output file specified for template_engine rule."
+            )
+        if len(input) != 1:
+            if "template" not in input.keys():
+                raise ValueError(
+                    "More than one input file specified for template engine rule, but no "
+                    "input file named as 'template'."
+                )
+            else:
+                self.input_file = input.template
+        else:
+            self.input_file = input[0]
+
+        self.input = input
         self.output_file = output[0]
         self.params = params
         self.wildcards = wildcards
@@ -18,24 +32,28 @@ def variables(self):
             "params": self.params,
             "wildcards": self.wildcards,
             "config": self.config,
+            "input": self.input,
         }
 
     @abstractmethod
     def render(self):
         ...
 
 
-def render_template(engine, input, output, params, wildcards, config):
-    if engine == "yte":
-        from snakemake.template_rendering.yte import YteRenderer
+def render_template(engine, input, output, params, wildcards, config, rule):
+    try:
+        if engine == "yte":
+            from snakemake.template_rendering.yte import YteRenderer
 
-        return YteRenderer(input, output, params, wildcards, config).render()
-    elif engine == "jinja2":
-        from snakemake.template_rendering.jinja2 import Jinja2Renderer
+            return YteRenderer(input, output, params, wildcards, config).render()
+        elif engine == "jinja2":
+            from snakemake.template_rendering.jinja2 import Jinja2Renderer
 
-        return Jinja2Renderer(input, output, params, wildcards, config).render()
-    else:
-        raise WorkflowError(
-            f"Unsupported template engine {engine}. "
-            "So far, only yte and jinja2 are supported."
-        )
+            return Jinja2Renderer(input, output, params, wildcards, config).render()
+        else:
+            raise WorkflowError(
+                f"Unsupported template engine {engine} in rule {rule}. "
+                "So far, only yte and jinja2 are supported."
+            )
+    except Exception as e:
+        raise WorkflowError(f"Error rendering template in rule {rule}.", e)

snakemake/workflow.py

@@ -1391,6 +1391,7 @@ def decorate(ruleinfo):
         )
         rule = self.get_rule(name)
         rule.is_checkpoint = checkpoint
+        rule.module_globals = self.modifier.globals
 
         def decorate(ruleinfo):
             nonlocal name