diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
new file mode 100644
index 0000000..6f7efed
--- /dev/null
+++ b/.github/CONTRIBUTING.md
@@ -0,0 +1,262 @@
+# Contributing to XAVIER
+
+## Proposing changes with issues
+
+If you want to make a change, it's a good idea to first
+[open an issue](https://code-review.tidyverse.org/issues/)
+and make sure someone from the team agrees that it’s needed.
+
+If you've decided to work on an issue,
+[assign yourself to the issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/assigning-issues-and-pull-requests-to-other-github-users#assigning-an-individual-issue-or-pull-request)
+so others will know you're working on it.
+
+## Pull request process
+
+We use [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+as our collaboration process.
+Follow the steps below for detailed instructions on contributing changes to
+XAVIER.
+
+![GitHub Flow diagram](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/GitHub-Flow_bg-white.png)
+
+### Clone the repo
+
+If you are a member of [CCBR](https://github.com/CCBR),
+you can clone this repository to your computer or development environment.
+Otherwise, you will first need to
+[fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo)
+the repo and clone your fork. You only need to do this step once.
+
+```sh
+git clone https://github.com/CCBR/XAVIER
+```
+
+> Cloning into 'XAVIER'... <br>
+> remote: Enumerating objects: 1136, done. <br>
+> remote: Counting objects: 100% (463/463), done. <br>
+> remote: Compressing objects: 100% (357/357), done. <br>
+> remote: Total 1136 (delta 149), reused 332 (delta 103), pack-reused 673 <br>
+> Receiving objects: 100% (1136/1136), 11.01 MiB | 9.76 MiB/s, done. <br>
+> Resolving deltas: 100% (530/530), done. <br>
+
+```sh
+cd XAVIER
+```
+
+### If this is your first time cloning the repo, you may need to install dependencies
+
+- Install snakemake and singularity or docker if needed (biowulf already has these available as modules).
+
+- Install the python dependencies with pip
+
+  ```sh
+  pip install .
+  ```
+
+  If you're developing on biowulf, you can use our shared conda environment which already has these dependencies installed
+
+  ```sh
+  . "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
+  conda activate py311
+  ```
+
+- Install [`pre-commit`](https://pre-commit.com/#install) if you don't already
+  have it. Then from the repo's root directory, run
+
+  ```sh
+  pre-commit install
+  ```
+
+  This will install the repo's pre-commit hooks.
+  You'll only need to do this step the first time you clone the repo.
+
+### Create a branch
+
+Create a Git branch for your pull request (PR). Give the branch a descriptive
+name for the changes you will make, such as `iss-10` if it is for a specific
+issue.
+
+```sh
+# create a new branch and switch to it
+git branch iss-10
+git switch iss-10
+```
+
+> Switched to a new branch 'iss-10'
+
+### Make your changes
+
+Edit the code, write and run tests, and update the documentation as needed.
+
+#### test
+
+Changes to the **python package** code will also need unit tests to demonstrate
+that the changes work as intended.
+We write unit tests with pytest and store them in the `tests/` subdirectory.
+Run the tests with `python -m pytest`.
+
+If you change the **workflow**, please run the workflow with the test profile
+and make sure your new feature or bug fix works as intended.
+
+#### document
+
+If you have added a new feature or changed the API of an existing feature,
+you will likely need to update the documentation in `docs/`.
+
+### Commit and push your changes
+
+If you're not sure how often you should commit or what your commits should
+consist of, we recommend following the "atomic commits" principle where each
+commit contains one new feature, fix, or task.
+Learn more about atomic commits here:
+<https://www.freshconsulting.com/insights/blog/atomic-commits/>
+
+First, add the files that you changed to the staging area:
+
+```sh
+git add path/to/changed/files/
+```
+
+Then make the commit.
+Your commit message should follow the
+[Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/)
+specification.
+Briefly, each commit should start with one of the approved types such as
+`feat`, `fix`, `docs`, etc. followed by a description of the commit.
+Take a look at the [Conventional Commits specification](https://www.conventionalcommits.org/en/v1.0.0/#summary)
+for more detailed information about how to write commit messages.
+
+```sh
+git commit -m 'feat: create function for awesome feature'
+```
+
+pre-commit will enforce that your commit message and the code changes are
+styled correctly and will attempt to make corrections if needed.
+
+> Check for added large files..............................................Passed <br>
+> Fix End of Files.........................................................Passed <br>
+> Trim Trailing Whitespace.................................................Failed <br>
+>
+> - hook id: trailing-whitespace <br>
+> - exit code: 1 <br>
+> - files were modified by this hook <br> > <br>
+>   Fixing path/to/changed/files/file.txt <br> > <br>
+>   codespell................................................................Passed <br>
+>   style-files..........................................(no files to check)Skipped <br>
+>   readme-rmd-rendered..................................(no files to check)Skipped <br>
+>   use-tidy-description.................................(no files to check)Skipped <br>
+
+In the example above, one of the hooks modified a file in the proposed commit,
+so the pre-commit check failed. You can run `git diff` to see the changes that
+pre-commit made and `git status` to see which files were modified. To proceed
+with the commit, re-add the modified file(s) and re-run the commit command:
+
+```sh
+git add path/to/changed/files/file.txt
+git commit -m 'feat: create function for awesome feature'
+```
+
+This time, all the hooks either passed or were skipped
+(e.g. hooks that only run on R code will not run if no R files were
+committed).
+When the pre-commit check is successful, the usual commit success message
+will appear after the pre-commit messages showing that the commit was created.
+
+> Check for added large files..............................................Passed <br>
+> Fix End of Files.........................................................Passed <br>
+> Trim Trailing Whitespace.................................................Passed <br>
+> codespell................................................................Passed <br>
+> style-files..........................................(no files to check)Skipped <br>
+> readme-rmd-rendered..................................(no files to check)Skipped <br>
+> use-tidy-description.................................(no files to check)Skipped <br>
+> Conventional Commit......................................................Passed <br> > [iss-10 9ff256e] feat: create function for awesome feature <br>
+> 1 file changed, 22 insertions(+), 3 deletions(-) <br>
+
+Finally, push your changes to GitHub:
+
+```sh
+git push
+```
+
+If this is the first time you are pushing this branch, you may have to
+explicitly set the upstream branch:
+
+```sh
+git push --set-upstream origin iss-10
+```
+
+> Enumerating objects: 7, done. <br>
+> Counting objects: 100% (7/7), done. <br>
+> Delta compression using up to 10 threads <br>
+> Compressing objects: 100% (4/4), done. <br>
+> Writing objects: 100% (4/4), 648 bytes | 648.00 KiB/s, done. <br>
+> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0 <br>
+> remote: Resolving deltas: 100% (3/3), completed with 3 local objects. <br>
+> remote: <br>
+> remote: Create a pull request for 'iss-10' on GitHub by visiting: <br>
+> remote: https://github.com/CCBR/XAVIER/pull/new/iss-10 <br>
+> remote: <br>
+> To https://github.com/CCBR/XAVIER <br> > <br> > [new branch] iss-10 -> iss-10 <br>
+> branch 'iss-10' set up to track 'origin/iss-10'. <br>
+
+We recommend pushing your commits often so they will be backed up on GitHub.
+You can view the files in your branch on GitHub at
+`https://github.com/CCBR/XAVIER/tree/<your-branch-name>`
+(replace `<your-branch-name>` with the actual name of your branch).
+
+### Create the PR
+
+Once your branch is ready, create a PR on GitHub:
+<https://github.com/CCBR/XAVIER/pull/new/>
+
+Select the branch you just pushed:
+
+![Create a new PR from your branch](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/new-PR.png)
+
+Edit the PR title and description.
+The title should briefly describe the change.
+Follow the comments in the template to fill out the body of the PR, and
+you can delete the comments (everything between `<!--` and `-->`) as you go.
+Be sure to fill out the checklist, checking off items as you complete them or
+striking through any irrelevant items.
+When you're ready, click 'Create pull request' to open it.
+
+![Open the PR after editing the title and description](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/create-PR.png)
+
+Optionally, you can mark the PR as a draft if you're not yet ready for it to
+be reviewed, then change it later when you're ready.
+
+### Wait for a maintainer to review your PR
+
+We will do our best to follow the tidyverse code review principles:
+<https://code-review.tidyverse.org/>.
+The reviewer may suggest that you make changes before accepting your PR in
+order to improve the code quality or style.
+If that's the case, continue to make changes in your branch and push them to
+GitHub, and they will appear in the PR.
+
+Once the PR is approved, the maintainer will merge it and the issue(s) the PR
+links will close automatically.
+Congratulations and thank you for your contribution!
+
+### After your PR has been merged
+
+After your PR has been merged, update your local clone of the repo by
+switching to the main branch and pulling the latest changes:
+
+```sh
+git checkout main
+git pull
+```
+
+It's a good idea to run `git pull` before creating a new branch so it will
+start from the most recent commits in main.
+
+## Helpful links for more information
+
+- [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+- [semantic versioning guidelines](https://semver.org/)
+- [changelog guidelines](https://keepachangelog.com/en/1.1.0/)
+- [tidyverse code review principles](https://code-review.tidyverse.org)
+- [reproducible examples](https://www.tidyverse.org/help/#reprex)
+- [nf-core extensions for VS Code](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack)
diff --git a/.github/workflows/build-docker-meta.yml b/.github/workflows/build-docker-meta.yml
new file mode 100644
index 0000000..87a61bc
--- /dev/null
+++ b/.github/workflows/build-docker-meta.yml
@@ -0,0 +1,46 @@
+name: build-docker-meta
+
+on:
+  workflow_dispatch:
+    inputs:
+      context_dir:
+        type: string
+        description: path to the directory containing the Dockerfile and meta.yml file (e.g. common/ccbr_chipseeker/)
+        required: true
+      push:
+        type: boolean
+        description: Push to DockerHub (uncheck to only build the container without pushing)
+        required: true
+        default: true
+
+jobs:
+  build-docker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pietrobolcato/action-read-yaml@1.0.0
+        id: metadata
+        with:
+          config: ${{ github.workspace }}/${{ github.event.inputs.context_dir }}/meta.yml
+      - name: Login to DockerHub
+        if: ${{ github.event.inputs.push == 'true' }}
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Prepare build-time variables
+        id: vars
+        run: |
+          echo "DATE=$(date +"%Y-%m-%d")" >> "$GITHUB_OUTPUT"
+      - 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: ${{ github.event.inputs.context_dir }}
+          push: ${{ github.event.inputs.push }}
+          tags: ${{ steps.metadata.outputs['container'] }}
+          build-args: |
+            BUILD_DATE=${{ steps.vars.outputs.DATE }}
+            BUILD_TAG=${{ steps.metadata.outputs['version'] }}
+            REPONAME=${{ steps.metadata.outputs['image_name'] }}
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
new file mode 100644
index 0000000..de1d9f8
--- /dev/null
+++ b/.github/workflows/docker.yml
@@ -0,0 +1,64 @@
+name: docker
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "docker/**"
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "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 }}
+          # only push container to docker hub if not triggered from a PR
+          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/CHANGELOG.md b/CHANGELOG.md
index 92263d0..d42f36c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,7 +1,16 @@
 ## XAVIER development version
 
+- Fix minor bug in assess_significance.R script associated with rule freec_exome_somatic (#120, @samarth8392)
 - Fix `cache` subcommand to correctly read the container images config file. (#124, @kelly-sovacool)
 
+## XAVIER 3.1.1
+
+- New contributing guide available on GitHub and the documentation website. (#114, @kelly-sovacool)
+- New `xavier debug` subcommand to determine the base directory for debugging purposes. (#114, @kelly-sovacool)
+- Upgraded `ccbr_wes_base` docker to v1.1.0 with updated GATK version to v4.6.0.0 (#116, @samarth8392)
+- Upgrade multiqc container to use v1.15. (#117, @kelly-sovacool)
+- Upgrade memory for rule "bwa_mem" to 100G (#118, @samarth8392)
+
 ## XAVIER 3.1.0
 
 ### new features
diff --git a/CITATION.cff b/CITATION.cff
index c8f815c..ecee53e 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -46,5 +46,5 @@ identifiers:
   - description: Archived snapshots of all versions
     type: doi
     value: 10.5281/zenodo.12727315
-version: v3.1.0
-date-released: "2024-08-27"
+version: v3.1.1
+date-released: "2024-10-02"
diff --git a/VERSION b/VERSION
index 0f9d6b1..8d70082 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-3.1.0-dev
+3.1.1-dev
diff --git a/config/cluster.biowulf.json b/config/cluster.biowulf.json
index a647265..7856824 100644
--- a/config/cluster.biowulf.json
+++ b/config/cluster.biowulf.json
@@ -120,7 +120,7 @@
     },
     "bwa_mem": {
         "threads": "24",
-        "mem": "64G"
+        "mem": "100G"
     },
     "picard_headers": {
         "threads": "2",
diff --git a/config/cluster.frce.json b/config/cluster.frce.json
index 6c7773d..1fe95e1 100644
--- a/config/cluster.frce.json
+++ b/config/cluster.frce.json
@@ -119,7 +119,7 @@
     },
     "bwa_mem": {
         "threads": "24",
-        "mem": "64G"
+        "mem": "100G"
     },
     "picard_headers": {
         "threads": "2",
diff --git a/config/containers/images.json b/config/containers/images.json
index 7c35a96..68f2ddd 100644
--- a/config/containers/images.json
+++ b/config/containers/images.json
@@ -1,6 +1,6 @@
 {
     "images": {
-        "wes_base": "docker://nciccbr/ccbr_wes_base:v0.1.0",
+        "wes_base": "docker://nciccbr/ccbr_wes_base:1.1.0",
         "vcf2maf": "docker://dnousome/ccbr_vcf2maf:v102.0.0",
         "mutect": "docker://nciccbr/ccbr_mutect:v0.1.0",
         "fastq_screen": "docker://nciccbr/ccbr_fastq_screen_0.13.0:v2.0",
@@ -8,7 +8,7 @@
         "fastqvalidator": "docker://nciccbr/ccbr_fastqvalidator:v0.1.0",
         "kraken": "docker://nciccbr/ccbr_kraken_v2.1.1:v0.0.1",
         "miniconda": "docker://continuumio/miniconda3:4.9.2",
-        "multiqc": "docker://nciccbr/ccbr_multiqc_1.9:v0.0.1",
+        "multiqc": "docker://nciccbr/ccbr_multiqc_1.15:v1",
         "picard": "docker://nciccbr/ccbr_picard:v0.0.1",
         "python": "docker://nciccbr/ccbr_python:v0.0.1",
         "qualimap": "docker://nciccbr/ccbr_qualimap:v0.0.1"
diff --git a/docker/wes_base/Dockerfile b/docker/wes_base/Dockerfile
index 209eadd..dff757b 100644
--- a/docker/wes_base/Dockerfile
+++ b/docker/wes_base/Dockerfile
@@ -1,7 +1,14 @@
 # Base image
-FROM ubuntu:20.04
+FROM nciccbr/ccbr_ubuntu_base_20.04:v6
 
-MAINTAINER <vishal.koparde@nih.gov, kuhnsa@nih.gov>
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+LABEL maintainer <vishal.koparde@nih.gov, kuhnsa@nih.gov>
 
 # Create Container filesystem specific
 # working directory and opt directories
@@ -38,11 +45,12 @@ RUN apt-get update \
       python3 \
       python3-pip \
       unzip \
-      wget
+      wget \
+      less
 
 # Make python3 the default interpreter
 # and install Python Packages
-RUN ln -s /usr/bin/python3.8 /usr/bin/python
+#RUN ln -s /usr/bin/python3.8 /usr/bin/python
 RUN pip3 install --upgrade pip \
 	  && pip3 install argparse \
 	  && pip3 install numpy \
@@ -89,7 +97,14 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -y \
       manpages-dev \
       zlib1g \
       zlib1g-dev \
-      zlibc
+      zlibc \
+      openjdk-17-jdk \
+      openjdk-11-jdk
+
+# Install Java 17
+# RUN apt-get update && apt-get install -y openjdk-17-jdk
+# ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64
+# ENV PATH="$JAVA_HOME/bin:${PATH}"
 
 # Common bioinformatics tools
 # bwa/0.7.17  bowtie/1.2.3  bowtie2/2.3.5.1
@@ -115,13 +130,13 @@ RUN wget https://github.com/biod/sambamba/releases/download/v0.8.1/sambamba-0.8.
     && mv /opt2/sambamba-0.8.1-linux-amd64-static /opt2/sambamba \
     && chmod a+rx /opt2/sambamba
 
-# Install GATK4 (GATK/4.2.2.0)
-# Requires Java8 or 1.8
-RUN wget https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip \
-    && unzip /opt2/gatk-4.2.2.0.zip \
-    && rm /opt2/gatk-4.2.2.0.zip \
-    && /opt2/gatk-4.2.2.0/gatk --list
-ENV PATH="/opt2/gatk-4.2.2.0:$PATH"
+# Install GATK4 (GATK/4.6.0.0)
+# Requires Java17
+RUN wget https://github.com/broadinstitute/gatk/releases/download/4.6.0.0/gatk-4.6.0.0.zip \
+    && unzip /opt2/gatk-4.6.0.0.zip \
+    && rm /opt2/gatk-4.6.0.0.zip \
+    && /opt2/gatk-4.6.0.0/gatk --list
+ENV PATH="/opt2/gatk-4.6.0.0:$PATH"
 
 # Install last release of GATK3 (GATK/3.8-1)
 # Only being used for the CombineVariants
@@ -175,12 +190,12 @@ RUN pip3 install --upgrade pip \
 RUN wget https://github.com/brentp/somalier/releases/download/v0.2.13/somalier \
     && chmod a+rx /opt2/somalier
 
-# Install VarScan/v2.4.4
+# Install VarScan/v2.4.6
 # Works with java8
 # and each wrapper script similar to HPC module
-RUN wget https://github.com/dkoboldt/varscan/raw/master/VarScan.v2.4.4.jar \
+RUN wget https://github.com/dkoboldt/varscan/raw/master/VarScan.v2.4.6.jar \
     && echo '#!/bin/bash' > /opt2/varscan \
-    && echo 'java -jar /opt2/VarScan.v2.4.4.jar  "$@"' >> /opt2/varscan \
+    && echo 'java8 -jar /opt2/VarScan.v2.4.6.jar  "$@"' >> /opt2/varscan \
     && chmod a+rx /opt2/varscan
 
 # Install snpEff/4.3t
@@ -195,7 +210,7 @@ ENV SNPEFF_JAR="/opt2/snpEff/snpEff.jar"
 
 # Install samblaster/0.1.26
 # Requires g++ and make (already satisfied)
-RUN git clone git://github.com/GregoryFaust/samblaster.git \
+RUN git clone https://github.com/GregoryFaust/samblaster.git \
     && cd /opt2/samblaster \
     && make \
     && chmod a+rX /opt2/samblaster/samblaster
@@ -234,7 +249,7 @@ ENV PATH="/opt2/VarDict-1.8.2/bin:$PATH"
 # and set java8 as default with links
 # to alternative versions
 ADD Dockerfile /opt2/base_gatk4_wes.dockerfile
-COPY argparse.bash /opt2
+COPY /argparse.bash /opt2
 # Trimmomatic requires java11
 ENV TRIMMOMATIC_JAR="/usr/share/java/trimmomatic-0.39.jar"
 RUN echo '#!/bin/bash' > /opt2/trimmomatic \
@@ -242,9 +257,10 @@ RUN echo '#!/bin/bash' > /opt2/trimmomatic \
     && chmod +x /opt2/trimmomatic
 RUN chmod -R a+rX /opt2 \
     && chmod a+x /opt2/argparse.bash \
+    && ln -s /usr/lib/jvm/java-17-openjdk-amd64/bin/java /usr/bin/java17 \
     && ln -s /usr/lib/jvm/java-11-openjdk-amd64/bin/java /usr/bin/java11 \
     && ln -s /usr/lib/jvm/java-8-openjdk-amd64/bin/java /usr/bin/java8 \
-    && ln -fs /usr/lib/jvm/java-8-openjdk-amd64/bin/java /usr/bin/java
+    && ln -fs /usr/lib/jvm/java-17-openjdk-amd64/bin/java /usr/bin/java
 ENV PATH="/opt2:$PATH"
 ENV TRIMMOJAR="/usr/share/java/trimmomatic-0.39.jar"
 
@@ -260,3 +276,6 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -y \
     pandoc \
     && apt-get clean && apt-get purge \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
\ No newline at end of file
diff --git a/docker/wes_base/meta.yml b/docker/wes_base/meta.yml
new file mode 100644
index 0000000..5a252c9
--- /dev/null
+++ b/docker/wes_base/meta.yml
@@ -0,0 +1,4 @@
+dockerhub_namespace: nciccbr
+image_name: ccbr_wes_base
+version: 1.1.0
+container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/docs/contributing.md b/docs/contributing.md
new file mode 100644
index 0000000..773a7e5
--- /dev/null
+++ b/docs/contributing.md
@@ -0,0 +1,3 @@
+--8<-- ".github/CONTRIBUTING.md"
+
+<!-- the contents are automatically inserted here. do not edit this file, instead edit the file specified above to make changes. -->
diff --git a/mkdocs.yml b/mkdocs.yml
index 130fb76..b61d5a6 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -113,4 +113,5 @@ nav:
       - Output Files: pipeline-details/output.md
   - FAQ:
       - General Questions: faq/questions.md
+      - How to contribute: contributing.md
   - License: license.md
diff --git a/pyproject.toml b/pyproject.toml
index 3e53d62..0f12601 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,7 +42,6 @@ dependencies = [
     "Click >= 8.1.3",
     "PySimpleGui < 5",
     "snakemake >= 7.32, < 8",
-    "snaketool-utils >= 0.0.5",
 ]
 
 [project.optional-dependencies]
diff --git a/src/xavier/__main__.py b/src/xavier/__main__.py
index 621fcfe..fdf1761 100755
--- a/src/xavier/__main__.py
+++ b/src/xavier/__main__.py
@@ -658,8 +658,15 @@ def parsed_arguments():
         help="Only display what remote resources would be pulled.",
     )
 
+    subparser_debug = subparsers.add_parser(
+        "debug",
+        help="Debug the pipeline base directory.",
+        usage=argparse.SUPPRESS,
+    )
+
     # Define handlers for each sub-parser
     subparser_run.set_defaults(func=run)
+    subparser_debug.set_defaults(func=debug)
     subparser_unlock.set_defaults(func=unlock)
     subparser_cache.set_defaults(func=cache)
     subparser_gui.set_defaults(func=launch_gui)
@@ -669,6 +676,11 @@ def parsed_arguments():
     return args
 
 
+def debug(args):
+    print("BASE:", xavier_base())
+    print(get_version(debug=True))
+
+
 def main():
     # show helpful error message when no arguments given
     if len(sys.argv) == 1:
diff --git a/src/xavier/util.py b/src/xavier/util.py
index 4f04bfa..d62a338 100644
--- a/src/xavier/util.py
+++ b/src/xavier/util.py
@@ -22,10 +22,13 @@ def xavier_base(*paths):
     return str(basedir.joinpath(*paths))
 
 
-def get_version():
+def get_version(debug=False):
     """Get the current version
     @return version <str>
     """
-    with open(xavier_base("VERSION"), "r") as vfile:
+    version_file = xavier_base("VERSION")
+    if debug:
+        print("VERSION FILE:", version_file)
+    with open(version_file, "r") as vfile:
         version = f"v{vfile.read().strip()}"
     return version
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 2196e3f..99abb44 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -33,6 +33,11 @@ def test_help():
     assert "XAVIER" in shell_run("./bin/xavier --help")
 
 
+def test_debug():
+    out = shell_run("./bin/xavier debug")
+    assert all(["xavier (v" in out, "BASE: /" in out, "VERSION FILE: /" in out])
+
+
 def test_dryrun_targets():
     if get_hpcname() == "biowulf":
         output_human, config_human = run_in_temp(f"{xavier_run} --genome hg38")
diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
index b5f1eaa..1e45b6c 100644
--- a/workflow/rules/qc.smk
+++ b/workflow/rules/qc.smk
@@ -390,7 +390,7 @@ rule snpeff:
     envmodules: config['tools']['snpEff']['modname']
     container: config['images']['wes_base']
     shell: """
-    java -Xmx12g -jar $SNPEFF_JAR \\
+    java8 -Xmx12g -jar $SNPEFF_JAR \\
         -v -canon -c {params.config} \\
         -csvstats {output.csv} \\
         -stats {output.html} \\
diff --git a/workflow/rules/somatic_snps.common.smk b/workflow/rules/somatic_snps.common.smk
index 27e6989..121b2c7 100644
--- a/workflow/rules/somatic_snps.common.smk
+++ b/workflow/rules/somatic_snps.common.smk
@@ -168,7 +168,7 @@ rule somatic_merge_callers:
       mkdir -p "$(dirname {output.mergedvcf})"
     fi
 
-    java -Xmx60g -Djava.io.tmpdir=${{tmp}} -jar $GATK_JAR -T CombineVariants \\
+    java8 -Xmx60g -Djava.io.tmpdir=${{tmp}} -jar $GATK_JAR -T CombineVariants \\
         -R {params.genome} \\
         -nt {threads} \\
         --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED \\
diff --git a/workflow/rules/somatic_snps.paired.smk b/workflow/rules/somatic_snps.paired.smk
index 1f5427b..42e902e 100644
--- a/workflow/rules/somatic_snps.paired.smk
+++ b/workflow/rules/somatic_snps.paired.smk
@@ -147,7 +147,7 @@ rule strelka:
     cd "$myoutdir"
     ./runWorkflow.py -m local -j {threads}
 
-    java -Xmx12g -Djava.io.tmpdir=${{tmp}} -XX:ParallelGCThreads={threads} \\
+    java8 -Xmx12g -Djava.io.tmpdir=${{tmp}} -XX:ParallelGCThreads={threads} \\
         -jar $GATK_JAR -T CombineVariants \\
         -R {params.genome} \\
         --variant results/variants/somatic.snvs.vcf.gz \\
@@ -439,7 +439,7 @@ rule varscan_paired:
     awk '{{gsub(/\y[W|K|Y|R|S|M|B|D|H|V]\y/,"N",$4); OFS = "\t"; print}}' {output.vcf}.indel \\
         | sed '/^$/d' > {output.vcf}.indel_temp
 
-    java -Xmx12g -Djava.io.tmpdir=${{tmp}} -XX:ParallelGCThreads={threads} \\
+    java8 -Xmx12g -Djava.io.tmpdir=${{tmp}} -XX:ParallelGCThreads={threads} \\
         -jar $GATK_JAR -T CombineVariants \\
         -R {params.genome} \\
         --variant {output.vcf}.snp_temp \\
diff --git a/workflow/scripts/assess_significance.R b/workflow/scripts/assess_significance.R
index e32f7f7..3e64bc4 100644
--- a/workflow/scripts/assess_significance.R
+++ b/workflow/scripts/assess_significance.R
@@ -48,7 +48,7 @@ for (i in c(1:length(cnvs[, 1]))) {
   }
   KS <- function(values, normals) {
     resultks <- try(ks.test(values, score(normals)), silent = TRUE)
-    if (class(resultks) == "try-error") {
+    if (paste(class(resultks), collapse="_") == "try-error") {
       return(list("statistic" = NA, "p.value" = NA, "alternative" = NA, "method" = NA, "data.name" = NA))
     } else {
       resultks