diff --git a/docs/bids_app/config.md b/docs/bids_app/config.md
index 8e2c45a5..fe96f460 100644
--- a/docs/bids_app/config.md
+++ b/docs/bids_app/config.md
@@ -40,7 +40,7 @@ The value of `filters` should be a dictionary where each key corresponds to a BI
   ```
   The above example selects all paths in the `func/` datatype folder that have a `_desc-` entity but do not have the `_acq-` entity.
 
-* [`list`](#list): Specify multiple string or boolean filters. Any path matching any one of the filters will be selected. Using `False` as one of the filters allows the entity to optionally be absent in addition to matching one of the string filters. Using `True` along with text is redundant, as `True` will cause any value to be selected. Using `True` with `False` is equivalent to not providing the filter at all.
+* [`list`](inv:*:py#list): Specify multiple string or boolean filters. Any path matching any one of the filters will be selected. Using `False` as one of the filters allows the entity to optionally be absent in addition to matching one of the string filters. Using `True` along with text is redundant, as `True` will cause any value to be selected. Using `True` with `False` is equivalent to not providing the filter at all.
 
   These filters:
 
diff --git a/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md
index 4ebfb83a..617af257 100644
--- a/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md	
+++ b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md	
@@ -1,7 +1,7 @@
 # Snakemake Command line interface
 
 ```{argparse}
-:module: snakemake
+:module: snakebids.snakemake_compat
 :func: get_argument_parser
 :prog: snakemake
 ```
diff --git a/snakebids/snakemake_compat.py b/snakebids/snakemake_compat.py
index 48abe810..db7cc5f6 100644
--- a/snakebids/snakemake_compat.py
+++ b/snakebids/snakemake_compat.py
@@ -1,12 +1,12 @@
 # type: ignore
 
 try:
-    from snakemake.cli import main
+    from snakemake.cli import get_argument_parser, main
     from snakemake.common import configfile
     from snakemake.common.configfile import load_configfile
 except ImportError:
     import snakemake.io as configfile
-    from snakemake import main
+    from snakemake import get_argument_parser, main
     from snakemake.io import load_configfile
 
 from snakemake.exceptions import WildcardError
@@ -20,4 +20,5 @@
     "Snakemake",
     "WildcardError",
     "configfile",
+    "get_argument_parser",
 ]
diff --git a/snakebids/snakemake_compat.pyi b/snakebids/snakemake_compat.pyi
index 887438ef..4f15a0cf 100644
--- a/snakebids/snakemake_compat.pyi
+++ b/snakebids/snakemake_compat.pyi
@@ -1,3 +1,4 @@
+from argparse import ArgumentParser
 from pathlib import Path
 from typing import Any, Callable, Iterable, Sequence
 
@@ -45,3 +46,4 @@ class Snakemake:
     params: Params[str]
 
 def main(argv: list[str] = ...) -> None: ...
+def get_argument_parser(profiles: list[str] | None = ...) -> ArgumentParser: ...