diff --git a/src/styx/compiler/compile/inputs.py b/src/styx/compiler/compile/inputs.py
index 035d7a1..97be9d8 100644
--- a/src/styx/compiler/compile/inputs.py
+++ b/src/styx/compiler/compile/inputs.py
@@ -236,7 +236,7 @@ def _bt_template_str_parse(
     """Parse a Boutiques command line template string into segments."""
     bt_template_str = boutiques_split_command(input_command_line_template)
 
-    bt_id_inputs = {input_.data.template_key: input_ for input_ in inputs}
+    template_key_inputs = {input_.data.template_key: input_ for input_ in inputs}
 
     segments: list[list[str | WithSymbol[InputArgument]]] = []
 
@@ -250,13 +250,12 @@ def _bt_template_str_parse(
             token = stack.pop()
             if isinstance(token, str):
                 any_match = False
-                for _, bt_input in bt_id_inputs.items():
-                    value_key = bt_input.data.internal_id
-                    if value_key == token:
+                for template_key, bt_input in template_key_inputs.items():
+                    if template_key == token:
                         stack.append(bt_input)
                         any_match = True
                         break
-                    o = token.split(value_key, 1)
+                    o = token.split(template_key, 1)
                     if len(o) == 2:
                         stack.append(o[0])
                         stack.append(bt_input)
diff --git a/src/styx/compiler/compile/outputs.py b/src/styx/compiler/compile/outputs.py
index 93360ad..1e1cf0f 100644
--- a/src/styx/compiler/compile/outputs.py
+++ b/src/styx/compiler/compile/outputs.py
@@ -1,5 +1,5 @@
 from styx.compiler.compile.common import SharedScopes, SharedSymbols
-from styx.model.core import InputArgument, OutputArgument, WithSymbol
+from styx.model.core import InputArgument, InputTypePrimitive, OutputArgument, WithSymbol
 from styx.pycodegen.core import PyFunc, PyModule, indent
 from styx.pycodegen.utils import as_py_literal, enbrace, enquote
 
@@ -18,6 +18,8 @@ def generate_outputs_definition(
             '"""',
             f"Output object returned when calling `{symbols.function}(...)`.",
             '"""',
+            "root: OutputPathType",
+            '"""Output root folder. This is the root folder for all outputs."""',
         ]),
     ])
     for out in outputs:
@@ -54,16 +56,34 @@ def generate_output_building(
 
     func.body.append(f"{symbols.ret} = {symbols.output_class}(")
 
+    # Set root output path
+    func.body.extend(indent([f'root={symbols.execution}.output_file("."),']))
+
     for out in outputs:
         strip_extensions = out.data.stripped_file_extensions is not None
         if out.data.path_template is not None:
             s = out.data.path_template
-            for a in inputs:
+            for input_ in inputs:
+                if input_.data.template_key not in s:
+                    continue
+
+                substitute = input_.symbol
+
+                if input_.data.type.primitive == InputTypePrimitive.File:
+                    # Just use the stem of the file
+                    # This is commonly used when output files 'inherit' the name of an input file
+                    substitute = f"pathlib.Path({substitute}).stem"
+                elif input_.data.type.primitive != InputTypePrimitive.String:
+                    raise Exception(
+                        f"Unsupported input type {input_.data.type.primitive} "
+                        f"for output path template of '{out.data.name}'."
+                    )
+
                 if strip_extensions:
                     exts = as_py_literal(out.data.stripped_file_extensions, "'")
-                    s = s.replace(f"{a.data.internal_id}", enbrace(f"{py_rstrip_fun}({a.symbol}, {exts})"))
-                else:
-                    s = s.replace(f"{a.data.internal_id}", enbrace(a.symbol))
+                    substitute = f"{py_rstrip_fun}({substitute}, {exts})"
+
+                s = s.replace(input_.data.template_key, enbrace(substitute))
 
             s_optional = ", optional=True" if out.data.optional else ""