diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..f78abe2
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,11 @@
+.git
+.github
+.ipython
+.jupyter
+.pytest_cache
+.venv
+.vscode
+CODE_OF_CONDUCT.md
+CONTRIBUTING.md
+Dockerfile
+LICENSE
diff --git a/Dockerfile b/Dockerfile
index 4b637a3..2087969 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -12,9 +12,6 @@ ENV DEBIAN_FRONTEND=noninteractive
 # add tini
 RUN apt-get update -y && apt-get install -y --no-install-recommends tini git
 
-# Install the project into `/app`
-WORKDIR /app
-
 # Enable bytecode compilation
 ENV UV_COMPILE_BYTECODE=1
 
@@ -27,6 +24,9 @@ ENV UV_NO_DEV=1
 # Ensure installed tools can be executed out of the box
 ENV UV_TOOL_BIN_DIR=/usr/local/bin
 
+# Install the project into `/app`
+WORKDIR /app
+
 # Install the project's dependencies using the lockfile and settings
 RUN --mount=type=cache,target=/root/.cache/uv \
     --mount=type=bind,source=uv.lock,target=uv.lock \
@@ -46,8 +46,7 @@ ENV PATH="/app/.venv/bin:$PATH"
 RUN groupadd --system --gid 999 nonroot \
  && useradd --system --gid 999 --uid 999 --create-home nonroot
 
+COPY --chmod=+x ./scripts/entrypoint.sh /app/
 # Use the non-root user to run our application
 USER nonroot
-
-# run the command using tini
-ENTRYPOINT ["/usr/bin/tini", "--"]
+ENTRYPOINT ["./entrypoint.sh"]
diff --git a/scripts/entrypoint.sh b/scripts/entrypoint.sh
new file mode 100755
index 0000000..c38a68f
--- /dev/null
+++ b/scripts/entrypoint.sh
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Ensure at least one argument is provided
+if [ "$#" -eq 0 ]; then
+  echo "Usage: $0 {uniref|uniprot} [args...]"
+  exit 1
+fi
+
+cmd="$1"
+shift
+
+case "$cmd" in
+  uniref)
+    # Run the uniref pipeline with any additional arguments via tini
+    exec /usr/bin/tini -- uv run uniref_pipeline "$@"
+    ;;
+  uniprot)
+    # Run the uniprot pipeline with any additional arguments via tini
+    exec /usr/bin/tini -- uv run uniprot_pipeline "$@"
+    ;;
+  *)
+    echo "Error: unknown command '$cmd'; valid commands are 'uniref' or 'uniprot'." >&2
+    exit 1
+    ;;
+esac