diff --git a/.github/workflows/docker_build_push.yml b/.github/workflows/docker_build_push.yml
index 87ebd3f9a..c94d28b2b 100644
--- a/.github/workflows/docker_build_push.yml
+++ b/.github/workflows/docker_build_push.yml
@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier]
+        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
     steps:
       - name: Git checkout
         id: git_checkout
diff --git a/.github/workflows/docker_build_push_release.yml b/.github/workflows/docker_build_push_release.yml
index caef83dd7..59c9dc7af 100644
--- a/.github/workflows/docker_build_push_release.yml
+++ b/.github/workflows/docker_build_push_release.yml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier]
+        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
     steps:
       - name: Git checkout
         id: git_checkout
diff --git a/.github/workflows/docker_build_push_release_submodules.yml b/.github/workflows/docker_build_push_release_submodules.yml
deleted file mode 100644
index 7bf3318f9..000000000
--- a/.github/workflows/docker_build_push_release_submodules.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-name: build and push container submodule
-# Trigger building and testing container only on pull requests
-on:
-  push:
-    tags:
-      - "**"
-
-jobs:
-  main:
-    name: Docker image build
-    runs-on: ubuntu-20.04
-    strategy:
-      fail-fast: false
-      matrix:
-        container-name: [ascatNgs]
-    steps:
-      - name: Git checkout
-        id: git_checkout
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-      - name: Get branch name
-        id: get_branch_name
-        shell: bash
-        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF##*/})"
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-      - name: Login to DockerHub
-        id: docker_login
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-      - name: Build and push
-        id: docker_build_and_push
-        uses: docker/build-push-action@v3
-        with:
-          context: submodules/${{ matrix.container-name }}
-          push: true
-          tags: clinicalgenomics/balsamic:release_${{ steps.get_branch_name.outputs.branch }}-${{ matrix.container-name }}
-          provenance: false
diff --git a/.github/workflows/docker_build_push_submodules.yml b/.github/workflows/docker_build_push_submodules.yml
deleted file mode 100644
index 16d1ec402..000000000
--- a/.github/workflows/docker_build_push_submodules.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-name: build test container submodule
-# Trigger building and testing container only on pull requests
-on:
-  push:
-    branches:
-      - master
-      - develop
-jobs:
-  main:
-    name: Docker image build
-    runs-on: ubuntu-20.04
-    strategy:
-      fail-fast: false
-      matrix:
-        container-name: [ascatNgs]
-    steps:
-      - name: Git checkout
-        id: git_checkout
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-      - name: Get branch name
-        id: get_branch_name
-        shell: bash
-        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF##*/})"
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-      - name: Login to DockerHub
-        id: docker_login
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-      - name: Build and push
-        id: docker_build_and_push
-        uses: docker/build-push-action@v3
-        with:
-          context: submodules/${{ matrix.container-name }}
-          push: true
-          tags: clinicalgenomics/balsamic:${{ steps.get_branch_name.outputs.branch }}-${{ matrix.container-name }}
-          provenance: false
diff --git a/.github/workflows/docker_build_test_pull_request.yml b/.github/workflows/docker_build_test_pull_request.yml
index 1f6d1a6f9..d6fe68bf8 100644
--- a/.github/workflows/docker_build_test_pull_request.yml
+++ b/.github/workflows/docker_build_test_pull_request.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier]
+        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
     steps:
       - name: Git checkout
         id: git_checkout
diff --git a/.github/workflows/docker_build_test_pull_request_submodules.yml b/.github/workflows/docker_build_test_pull_request_submodules.yml
deleted file mode 100644
index 01f22820d..000000000
--- a/.github/workflows/docker_build_test_pull_request_submodules.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: build test container submodule
-# Trigger building and testing container only on pull requests
-on:
-  push:
-    branches-ignore:
-      - master
-      - develop
-    tags-ignore:
-      - "**"
-jobs:
-  main:
-    name: Docker image build test
-    runs-on: ubuntu-20.04
-    strategy:
-      fail-fast: false
-      matrix:
-        container-name: [ascatNgs]
-    steps:
-      - name: Git checkout
-        id: git_checkout
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-      - name: Get branch name
-        id: get_branch_name
-        shell: bash
-        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF##*/})"
-      - name: Login to DockerHub
-        id: docker_login
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-      - name: Build only
-        id: docker_build_only
-        uses: docker/build-push-action@v3
-        with:
-          context: submodules/${{ matrix.container-name }}
-          push: false
-          tags: clinicalgenomics/balsamic:${{ steps.get_branch_name.outputs.branch }}-${{ matrix.container-name }}
diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index 002f077ce..000000000
--- a/.gitmodules
+++ /dev/null
@@ -1,3 +0,0 @@
-[submodule "submodules/ascatNgs"]
-	path = submodules/ascatNgs
-	url = https://github.com/cancerit/ascatNgs
diff --git a/BALSAMIC/containers/ascatNgs/Dockerfile b/BALSAMIC/containers/ascatNgs/Dockerfile
new file mode 100644
index 000000000..40f177082
--- /dev/null
+++ b/BALSAMIC/containers/ascatNgs/Dockerfile
@@ -0,0 +1,183 @@
+FROM quay.io/wtsicgp/pcap-core:5.4.2 AS builder
+
+USER root
+
+ENV VER_CGPVCF="v2.2.1"
+ENV VER_VCFTOOLS="0.1.16"
+ENV VER_ALLELECOUNT="v4.2.1"
+
+RUN apt-get -yq update
+RUN apt-get install -qy --no-install-recommends lsb-release
+RUN apt-get install -qy --no-install-recommends gnupg
+RUN apt-get install -yq --no-install-recommends dirmngr
+RUN apt-get install -yq --no-install-recommends wget
+RUN apt-get install -yq --no-install-recommends build-essential
+RUN apt-get install -yq --no-install-recommends ca-certificates
+RUN apt-get install -yq --no-install-recommends locales
+RUN apt-get install -yq --no-install-recommends g++
+RUN apt-get install -yq --no-install-recommends make
+RUN apt-get install -yq --no-install-recommends gcc
+RUN apt-get install -yq --no-install-recommends git
+
+ENV DEBIAN_FRONTEND "noninteractive"
+RUN apt-get -yq update
+RUN apt-get install -yq --no-install-recommends software-properties-common
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+RUN apt-get -yq update
+RUN apt-get install -yq --no-install-recommends locales
+RUN apt-get install -yq --no-install-recommends g++
+RUN apt-get install -yq --no-install-recommends make
+RUN apt-get install -yq --no-install-recommends gcc
+RUN apt-get install -yq --no-install-recommends wget
+RUN apt-get install -yq --no-install-recommends pkg-config
+RUN apt-get install -yq --no-install-recommends zlib1g-dev
+RUN apt-get install -yq --no-install-recommends libbz2-dev
+RUN apt-get install -yq --no-install-recommends unzip
+RUN apt-get install -yq --no-install-recommends libpng-dev
+RUN apt-get install -yq --no-install-recommends tzdata
+RUN apt-get install -yq --no-install-recommends libcurl4-openssl-dev
+RUN apt-get install -yq --no-install-recommends libxml2-dev
+RUN apt-get install -yq --no-install-recommends libgit2-dev
+RUN apt-get install -yq --no-install-recommends liblzma-dev
+RUN apt-get install -yq --no-install-recommends libssl-dev
+RUN apt-get install -yq --no-install-recommends nettle-dev
+RUN apt-get install -yq --no-install-recommends time
+RUN apt-get install -yq --no-install-recommends libcairo2-dev
+RUN apt-get install -yq --no-install-recommends gfortran
+RUN apt-get install -yq --no-install-recommends libblas-dev
+RUN apt-get install -yq --no-install-recommends libboost-all-dev
+RUN apt-get install -yq --no-install-recommends libpstreams-dev
+RUN apt-get install -yq --no-install-recommends cpanminus
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$PATH
+ENV PERL5LIB $OPT/lib/perl5
+ENV LD_LIBRARY_PATH $OPT/lib
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV R_LIBS $OPT/R-libs
+ENV R_LIBS_USER $R_LIBS
+ENV R_PROFILE_USER $OPT/config/Rprofile
+RUN mkdir -p $OPT
+RUN mkdir $OPT/config/
+RUN mkdir -p $R_LIBS_USER
+WORKDIR /R
+RUN cd /R && wget --progress=dot:giga -q -nv https://cdn.rstudio.com/r/ubuntu-2004/pkgs/r-4.2.1_1_amd64.deb &&\
+	apt-get install --no-install-recommends -f -y ./r-4.2.1_1_amd64.deb &&\
+	ln -s /opt/R/4.2.1/bin/R /usr/bin/R &&\
+    ln -s /opt/R/4.2.1/bin/Rscript /usr/bin/Rscript &&\
+    ln -s /opt/R/4.2.1/lib/R /usr/lib/R
+WORKDIR /git
+RUN cd /git && git clone --recursive https://github.com/cancerit/ascatNgs.git &&\
+   cd ascatNgs &&\
+   ./setup.sh $OPT
+
+USER    ubuntu
+FROM ubuntu:20.04
+
+RUN apt-get -yq update && \
+apt-get install -qy --no-install-recommends \
+lsb-release \
+gnupg \
+dirmngr \
+wget \
+build-essential \
+locales \
+gcc \
+wget \
+pkg-config \
+cpanminus \
+git \
+unattended-upgrades && \
+unattended-upgrade -d -v && \
+apt-get remove -yq unattended-upgrades && \
+apt-get autoremove -yq &&\
+apt-get clean && \
+rm -rf /var/lib/apt/lists/*
+
+ENV DEBIAN_FRONTEND "noninteractive"
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+RUN apt-get -yq update \
+&& apt-get install -yq --no-install-recommends \
+software-properties-common \
+libreadline6-dev \
+libx11-dev \
+libxt-dev \
+libpng-dev \
+libjpeg-dev \
+libcairo2-dev \
+libcairo2-dev \
+xvfb \
+libbz2-dev \
+libzstd-dev \
+liblzma-dev \
+libcurl4-openssl-dev \
+texinfo \
+texlive \
+texlive-fonts-extra \
+screen \
+libpcre2-dev \
+locales \
+curl \
+wget \
+ca-certificates \
+libperlio-gzip-perl \
+bzip2 \
+psmisc \
+time \
+zlib1g \
+liblzma5 \
+libncurses5 \
+p11-kit \
+libcurl3-gnutls \
+libcurl4 \
+moreutils \
+google-perftools \
+libcairo2 \
+gfortran \
+unattended-upgrades && \
+unattended-upgrade -d -v && \
+apt-get remove -yq unattended-upgrades && \
+apt-get autoremove -yq && \
+apt-get clean && \
+rm -rf /var/lib/apt/lists/*
+
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$PATH
+ENV PERL5LIB $OPT/lib/perl5
+ENV LD_LIBRARY_PATH $OPT/lib
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV R_LIBS $OPT/R-libs
+ENV R_LIBS_USER $R_LIBS
+ENV R_PROFILE_USER $OPT/config/Rprofile
+
+RUN mkdir -p $OPT
+COPY --from=builder $OPT $OPT
+COPY --from=builder /opt/R /opt/R
+WORKDIR /R
+RUN cd /R && wget --progress=dot:giga -q -nv https://cdn.rstudio.com/r/ubuntu-2004/pkgs/r-4.2.1_1_amd64.deb &&\
+	apt-get install --no-install-recommends -f -y ./r-4.2.1_1_amd64.deb
+RUN	ln -s /opt/R/4.2.1/bin/R /usr/bin/R
+RUN ln -s /opt/R/4.2.1/bin/Rscript /usr/bin/Rscript
+RUN ln -s /opt/R/4.2.1/lib/R /usr/lib/R
+RUN rm -rf /R
+RUN rm -rf /var/lib/apt/lists/*
+RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
+
+USER ubuntu
+WORKDIR /home/ubuntu
+
+CMD ["/bin/bash"]
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index a60a3a766..774843a7a 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -20,7 +20,7 @@ Fixed:
 * Bump cryptography to v40.0.2 and gsutil to v5.23 https://github.com/Clinical-Genomics/BALSAMIC/pull/1154
 * Pytest file saved in balsamic directory https://github.com/Clinical-Genomics/BALSAMIC/pull/1093
 * Fix varcall_py3 container bcftools dependency error https://github.com/Clinical-Genomics/BALSAMIC/pull/1097
-
+* AscatNgs container https://github.com/Clinical-Genomics/BALSAMIC/pull/1155
 
 [11.2.0]
 --------
diff --git a/container_tests/ascatNgs/ascatNgs.sh b/container_tests/ascatNgs/ascatNgs.sh
new file mode 100644
index 000000000..dafd7d6ee
--- /dev/null
+++ b/container_tests/ascatNgs/ascatNgs.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+# Test if commands exist
+
+valid_commands=( "ascat.pl" "R" )
+
+for valid_command in "${valid_commands[@]}"
+do
+  if ! command -v "${valid_command}" &> /dev/null
+  then
+    echo "${valid_command} could not be found"
+    exit 1
+  else
+    echo "${valid_command} command is found and valid"
+  fi
+done
+
diff --git a/submodules/ascatNgs b/submodules/ascatNgs
deleted file mode 160000
index 0d83b28d3..000000000
--- a/submodules/ascatNgs
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 0d83b28d3837d1d001c1dceefcd20b71aa351225