fix: fixed handling of input functions and unpack when using the prefix setting of module definitions

snakemake/path_modifier.py

@@ -5,7 +5,7 @@
 
 import os
 from snakemake.exceptions import WorkflowError
-from snakemake.io import is_flagged, AnnotatedString, flag, get_flag_value
+from snakemake.io import is_callable, is_flagged, AnnotatedString, flag, get_flag_value
 
 
 PATH_MODIFIER_FLAG = "path_modified"
@@ -57,6 +57,7 @@ def replace_prefix(self, path, property=None):
             or os.path.isabs(path)
             or path.startswith("..")
             or is_flagged(path, "remote_object")
+            or is_callable(path)
         ):
             # no replacement
             return path
@@ -78,9 +79,9 @@ def replace_prefix(self, path, property=None):
             else:
                 # no matching prefix
                 return path
-
-        # prefix case
-        return self.prefix + path
+        else:
+            # prefix case
+            return self.prefix + path
 
     def apply_default_remote(self, path):
         """Apply the defined default remote provider to the given path and return the updated _IOFile.

snakemake/rules.py

@@ -734,7 +734,7 @@ def apply_input_function(
         incomplete_checkpoint_func=lambda e: None,
         raw_exceptions=False,
         groupid=None,
-        **aux_params
+        **aux_params,
     ):
         incomplete = False
         if isinstance(func, _IOFile):
@@ -811,24 +811,27 @@ def _apply_wildcards(
                     incomplete_checkpoint_func=incomplete_checkpoint_func,
                     is_unpack=is_unpack,
                     groupid=groupid,
-                    **aux_params
+                    **aux_params,
                 )
 
             if is_unpack and not incomplete:
                 if not allow_unpack:
                     raise WorkflowError(
                         "unpack() is not allowed with params. "
                         "Simply return a dictionary which can be directly ."
-                        "used, e.g. via {params[mykey]}."
+                        "used, e.g. via {params[mykey]}.",
+                        rule=self,
                     )
                 # Sanity checks before interpreting unpack()
                 if not isinstance(item, (list, dict)):
                     raise WorkflowError(
-                        "Can only use unpack() on list and dict", rule=self
+                        f"Can only use unpack() on list and dict, but {item} was returned.",
+                        rule=self,
                     )
                 if name:
                     raise WorkflowError(
-                        "Cannot combine named input file with unpack()", rule=self
+                        f"Cannot combine named input file (name {name}) with unpack()",
+                        rule=self,
                     )
                 # Allow streamlined code with/without unpack
                 if isinstance(item, list):
@@ -1067,7 +1070,7 @@ def apply(name, res, threads=None):
                         attempt=attempt,
                         incomplete_checkpoint_func=lambda e: 0,
                         raw_exceptions=True,
-                        **aux
+                        **aux,
                     )
                 except (Exception, BaseException) as e:
                     raise InputFunctionException(e, rule=self, wildcards=wildcards)

tests/test_github_issue1498/Snakefile

@@ -0,0 +1,22 @@
+rule all:
+    input:
+        "results/all.done",
+
+
+module other:
+    snakefile:
+        "module.smk"
+    prefix:
+        "results/other"
+
+
+use rule * from other as other_*
+
+
+rule all_impl:
+    output:
+        out=touch("results/all.done"),
+    input:
+        b=rules.other_b.output.b,
+    shell:
+        "cp {input} {output}"

tests/test_github_issue1498/module.smk

@@ -0,0 +1,21 @@
+rule a:
+    output:
+        a=touch("results/a.txt"),
+
+
+def unpack_a(wildcards):
+    return {"a": rules.a.output.a}
+
+
+def lambda_a(wildcards):
+    return rules.a.output.a
+
+
+rule b:
+    input:
+        unpack(unpack_a),
+        # a = lambda_a,
+    output:
+        b="results/b.txt",
+    shell:
+        "cp {input.a} {output}"

tests/tests.py

@@ -1591,5 +1591,9 @@ def test_github_issue1542():
     run(dpath("test_github_issue1542"), dryrun=True)
 
 
+def test_github_issue1498():
+    run(dpath("test_github_issue1498"))
+
+
 def test_cleanup_metadata_fail():
     run(dpath("test09"), cleanup_metadata=["xyz"])