diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 65ce573..8086ad8 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -34,6 +34,7 @@ jobs:
         run: uv run make -C docs clean html
 
       - name: GitHub Pages action
+        if: github.event_name == 'push'
         uses: peaceiris/actions-gh-pages@v3.6.1
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/Dockerfile b/Dockerfile
index 4437740..bddc98a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 # Generated by Neurodocker and Reproenv.
 
-FROM debian:bullseye-slim
+FROM debian:bookworm-slim
 ENV LANG="en_US.UTF-8" \
     LC_ALL="en_US.UTF-8" \
     ND_ENTRYPOINT="/neurodocker/startup.sh"
@@ -38,6 +38,7 @@ RUN curl -fsSL https://deno.land/install.sh | env DENO_INSTALL=/usr/local sh -s
 RUN curl -LsSf https://astral.sh/uv/install.sh | env UV_INSTALL_DIR=/usr/local/bin INSTALLER_NO_MODIFY_PATH=1 sh
 ENV UV_LINK_MODE="copy"
 ENV UV_PYTHON_INSTALL_DIR="/opt/uv-python"
+ENV UV_PYTHON="3.11"
 ENV UV_PROJECT_ENVIRONMENT="/home/ffrprep/.venv"
 ENV PYTHONDONTWRITEBYTECODE="1"
 COPY [".", \
@@ -61,7 +62,7 @@ RUN printf '{ \
     { \
       "name": "from_", \
       "kwds": { \
-        "base_image": "debian:bullseye-slim" \
+        "base_image": "debian:bookworm-slim" \
       } \
     }, \
     { \
@@ -127,6 +128,12 @@ RUN printf '{ \
         "UV_PYTHON_INSTALL_DIR": "/opt/uv-python" \
       } \
     }, \
+    { \
+      "name": "env", \
+      "kwds": { \
+        "UV_PYTHON": "3.11" \
+      } \
+    }, \
     { \
       "name": "env", \
       "kwds": { \
diff --git a/Singularity.def b/Singularity.def
index 45be799..9bf8f7d 100644
--- a/Singularity.def
+++ b/Singularity.def
@@ -1,7 +1,7 @@
 # Generated by Neurodocker and Reproenv.
 
 Bootstrap: docker
-From: debian:bullseye-slim
+From: debian:bookworm-slim
 
 %files
 . /home/ffrprep
@@ -12,6 +12,7 @@ export LC_ALL="en_US.UTF-8"
 export ND_ENTRYPOINT="/neurodocker/startup.sh"
 export UV_LINK_MODE="copy"
 export UV_PYTHON_INSTALL_DIR="/opt/uv-python"
+export UV_PYTHON="3.11"
 export UV_PROJECT_ENVIRONMENT="/home/ffrprep/.venv"
 export PYTHONDONTWRITEBYTECODE="1"
 export IS_DOCKER="1"
@@ -78,7 +79,7 @@ printf '{ \
     { \
       "name": "from_", \
       "kwds": { \
-        "base_image": "debian:bullseye-slim" \
+        "base_image": "debian:bookworm-slim" \
       } \
     }, \
     { \
@@ -144,6 +145,12 @@ printf '{ \
         "UV_PYTHON_INSTALL_DIR": "/opt/uv-python" \
       } \
     }, \
+    { \
+      "name": "env", \
+      "kwds": { \
+        "UV_PYTHON": "3.11" \
+      } \
+    }, \
     { \
       "name": "env", \
       "kwds": { \
diff --git a/ffrprep/ffrprep_cli.py b/ffrprep/ffrprep_cli.py
index b9bd3db..c64c2cb 100644
--- a/ffrprep/ffrprep_cli.py
+++ b/ffrprep/ffrprep_cli.py
@@ -1561,8 +1561,10 @@ def get_parser():
         help=(
             "Reference channel(s) for re-referencing. Provide space-separated "
             "channel names (e.g. --ref_channels M1 M2). Use 'average' for "
-            "average reference. Comma-separated single-argument styles are "
-            "also accepted for backward compatibility (e.g. 'M1,M2')."
+            "average reference, or 'skip' if the data is already referenced "
+            "and should not be re-referenced. Comma-separated single-argument "
+            "styles are also accepted for backward compatibility (e.g. "
+            "'M1,M2')."
         ),
         nargs="+",
         type=str,
@@ -1813,6 +1815,10 @@ def parse_ref_channels(ref_str):
         # Already a sequence; ensure items are stripped and handle
         # comma-separated tokens inside any element for backward
         # compatibility (e.g. ['M1,M2'] -> ['M1','M2']).
+        if len(ref_str) == 1 and isinstance(ref_str[0], str) and ref_str[0].strip().lower() == "skip":
+            return []  # Data is already referenced; do not re-reference
+        if len(ref_str) == 1 and isinstance(ref_str[0], str) and ref_str[0].strip().lower() == "average":
+            return None  # Average reference
         out = []
         for item in ref_str:
             if isinstance(item, str) and "," in item:
@@ -1824,6 +1830,8 @@ def parse_ref_channels(ref_str):
     s = str(ref_str)
     if s.lower() == "average":
         return None  # Average reference
+    if s.lower() == "skip":
+        return []  # Data is already referenced; do not re-reference
     if "," in s:
         # Split and strip whitespace around channel names
         return [c.strip() for c in s.split(",") if c.strip()]
diff --git a/ffrprep/preproc.py b/ffrprep/preproc.py
index 9b521df..65bc329 100644
--- a/ffrprep/preproc.py
+++ b/ffrprep/preproc.py
@@ -587,7 +587,8 @@ def reference_data(eeg_data=None, ref_channels=None):
         Channels to be used as reference. If more than one channel
         in list, the average of the channels in `ref_channels` will
         be used as the reference. If `None`, all channels will be
-        averaged as the reference.
+        averaged as the reference. If an empty list, the data is
+        marked as already referenced and is not modified.
         Default = None.
 
     Returns
diff --git a/ffrprep/tests/test_cli.py b/ffrprep/tests/test_cli.py
index 892ca57..abec3d3 100644
--- a/ffrprep/tests/test_cli.py
+++ b/ffrprep/tests/test_cli.py
@@ -220,6 +220,13 @@ def test_parse_ref_channels_average():
     assert parse_ref_channels("Average") is None
 
 
+def test_parse_ref_channels_average_from_argparse_list():
+    """--ref_channels uses nargs='+', so real CLI usage always passes a
+    list (e.g. ['average']) rather than a bare string."""
+    assert parse_ref_channels(["average"]) is None
+    assert parse_ref_channels(["AVERAGE"]) is None
+
+
 def test_parse_ref_channels_single():
     assert parse_ref_channels("Cz") == "Cz"
     assert parse_ref_channels("TP9") == "TP9"
@@ -235,6 +242,20 @@ def test_parse_ref_channels_empty_string():
     assert parse_ref_channels("") is None
 
 
+def test_parse_ref_channels_skip():
+    """'skip' normalizes to [] (data already referenced; do not modify)."""
+    assert parse_ref_channels("skip") == []
+    assert parse_ref_channels("SKIP") == []
+    assert parse_ref_channels("Skip") == []
+
+
+def test_parse_ref_channels_skip_from_argparse_list():
+    """--ref_channels uses nargs='+', so real CLI usage always passes a
+    list (e.g. ['skip']) rather than a bare string."""
+    assert parse_ref_channels(["skip"]) == []
+    assert parse_ref_channels(["SKIP"]) == []
+
+
 # ---------------------------------------------------------------------------
 # run_ffrprep — mocked end-to-end behavior
 # ---------------------------------------------------------------------------
diff --git a/generate_images.sh b/generate_images.sh
index 35f9b04..fc94f91 100644
--- a/generate_images.sh
+++ b/generate_images.sh
@@ -25,7 +25,7 @@ INSTALL_GROUP_FLAG="--no-dev"
 
 generate_docker() {
   docker run --rm repronim/neurodocker:2.1.1 generate docker \
-    --base-image debian:bullseye-slim \
+    --base-image debian:bookworm-slim \
     --pkg-manager apt \
     --arg DEBIAN_FRONTEND=noninteractive \
     --install $OS_PACKAGES \
@@ -33,6 +33,7 @@ generate_docker() {
     --run "$UV_INSTALL" \
     --env UV_LINK_MODE=copy \
     --env UV_PYTHON_INSTALL_DIR=/opt/uv-python \
+    --env UV_PYTHON=3.11 \
     --env UV_PROJECT_ENVIRONMENT=/home/ffrprep/.venv \
     --env PYTHONDONTWRITEBYTECODE=1 \
     --copy . /home/ffrprep \
@@ -48,7 +49,7 @@ generate_docker() {
 
 generate_singularity() {
   docker run --rm repronim/neurodocker:2.1.1 generate singularity \
-    --base-image debian:bullseye-slim \
+    --base-image debian:bookworm-slim \
     --pkg-manager apt \
     --arg DEBIAN_FRONTEND=noninteractive \
     --install $OS_PACKAGES \
@@ -56,6 +57,7 @@ generate_singularity() {
     --run "$UV_INSTALL" \
     --env UV_LINK_MODE=copy \
     --env UV_PYTHON_INSTALL_DIR=/opt/uv-python \
+    --env UV_PYTHON=3.11 \
     --env UV_PROJECT_ENVIRONMENT=/home/ffrprep/.venv \
     --env PYTHONDONTWRITEBYTECODE=1 \
     --copy . /home/ffrprep \