diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
new file mode 100644
index 0000000..6eabdcb
--- /dev/null
+++ b/.github/workflows/docker.yml
@@ -0,0 +1,57 @@
+name: docker
+
+on:
+  push:
+    paths:
+      - .github/workflows/docker.yml
+      - "docker/**"
+  workflow_dispatch:
+
+jobs:
+  generate-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix-metadata: ${{ steps.metadata.outputs.matrix }}
+    steps:
+      - uses: hellofresh/action-changed-files@v3
+        id: metadata
+        with:
+          pattern: docker/(?P<image_dir>\w+)/.*
+          default-patterns: |
+            meta.yml
+            Dockerfile
+
+  update-docker:
+    needs: [generate-matrix]
+    strategy:
+      matrix: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata) }}
+    if: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata).include[0] }} # skip if the matrix is empty!
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pietrobolcato/action-read-yaml@1.0.0
+        id: metadata
+        with:
+          config: ${{ github.workspace }}/docker/${{ matrix.image_dir }}/meta.yml
+      - name: Get date
+        id: date
+        run: |
+          echo "DATE=$(date +"%Y-%m-%d")" >> $GITHUB_OUTPUT
+      - name: Login to DockerHub
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        # only try building & pushing the container if parsing the metadata worked
+        if: ${{ steps.metadata.outputs['container'] != '' }}
+        with:
+          context: docker/${{ matrix.image_dir }}
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.metadata.outputs['container'] }}
+          build-args: |
+            BUILD_DATE=${{ steps.date.outputs.DATE }}
+            BUILD_TAG=${{ steps.metadata.outputs['version'] }}
+            REPONAME=${{ steps.metadata.outputs['image_name'] }}
diff --git a/docker/README.md b/docker/README.md
new file mode 100644
index 0000000..8f06d03
--- /dev/null
+++ b/docker/README.md
@@ -0,0 +1,4 @@
+# Containers for CRUISE
+
+Dockerfiles to create containers for processes in this nextflow workflow.
+These containers are built and pushed to dockerhub automatically when files in this directory change.
diff --git a/docker/bagel/Dockerfile b/docker/bagel/Dockerfile
new file mode 100644
index 0000000..c4abb1f
--- /dev/null
+++ b/docker/bagel/Dockerfile
@@ -0,0 +1,30 @@
+FROM nciccbr/ccbr_ubuntu_base_20.04:v5
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+# download bagel scripts and install dependencies
+RUN python3 -m pip install --upgrade pip
+RUN pip3 install click numpy scipy scikit-learn
+ADD https://github.com/hart-lab/bagel/archive/refs/tags/v2.0-115.tar.gz /opt2
+WORKDIR /opt2
+RUN tar -xzvf v2.0-115.tar.gz && rm -f v2.0-115.tar.gz
+ENV PATH="${PATH}:/opt2/bagel-2.0-115"
+
+# cleanup etc
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+#COPY argparse.bash /opt2
+RUN chmod -R a+rx /opt2/argparse.bash
+ENV PATH="/opt2/:$PATH"
+RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    apt-get autoclean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/{apt,dpkg,cache,log}/
+WORKDIR /data2
diff --git a/docker/bagel/README.md b/docker/bagel/README.md
new file mode 100644
index 0000000..0c5cb74
--- /dev/null
+++ b/docker/bagel/README.md
@@ -0,0 +1 @@
+# Container for bagel processes in CRUISE
diff --git a/docker/bagel/meta.yml b/docker/bagel/meta.yml
new file mode 100644
index 0000000..75269f5
--- /dev/null
+++ b/docker/bagel/meta.yml
@@ -0,0 +1,4 @@
+dockerhub_namespace: kellysovacool
+image_name: bagel
+version: test
+container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/docker/drugz/Dockerfile b/docker/drugz/Dockerfile
new file mode 100644
index 0000000..35ee09f
--- /dev/null
+++ b/docker/drugz/Dockerfile
@@ -0,0 +1,31 @@
+FROM nciccbr/ccbr_ubuntu_base_20.04:v5
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+# download drugz script and install dependencies
+RUN python3 -m pip install --upgrade pip
+RUN pip3 install six numpy pandas scipy argparse
+ADD https://github.com/hart-lab/drugz/archive/refs/heads/master.zip /opt2
+WORKDIR /opt2
+RUN ls
+RUN unzip master.zip && rm -f master.zip
+ENV PATH="${PATH}:/opt2/drugz-master"
+
+# cleanup etc
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+#COPY argparse.bash /opt2
+RUN chmod -R a+rx /opt2/argparse.bash
+ENV PATH="/opt2/:$PATH"
+RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    apt-get autoclean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/{apt,dpkg,cache,log}/
+WORKDIR /data2
diff --git a/docker/drugz/README.md b/docker/drugz/README.md
new file mode 100644
index 0000000..0152b9a
--- /dev/null
+++ b/docker/drugz/README.md
@@ -0,0 +1,3 @@
+# drugz
+
+Container for drugz processes in CRUISE
diff --git a/docker/drugz/meta.yml b/docker/drugz/meta.yml
new file mode 100644
index 0000000..970d7b8
--- /dev/null
+++ b/docker/drugz/meta.yml
@@ -0,0 +1,4 @@
+dockerhub_namespace: kellysovacool
+image_name: drugz
+version: test
+container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/docker/mageck/Dockerfile b/docker/mageck/Dockerfile
new file mode 100644
index 0000000..e69de29