diff --git a/.github/workflows/containers.yaml b/.github/workflows/containers.yaml
new file mode 100644
index 00000000..fce92588
--- /dev/null
+++ b/.github/workflows/containers.yaml
@@ -0,0 +1,120 @@
+name: Containers
+
+on:
+  push:
+    tags:
+      - "**"
+    branches:
+      - "**"
+    paths:
+      - "build/containers/**"
+      - "core"
+      - "combination"
+
+jobs:
+  checks:
+    name: Run quality checks
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Install requirements
+        run: |
+          sc_version="stable" # or "v0.4.7", or "latest"
+          hl_version="v2.12.0"
+          case $( uname -m ) in
+            arm64 | aarch64 )
+              sc_platform=aarch64
+              hl_platform=arm64
+              ;;
+            *)
+              sc_platform=$( uname -m )
+              hl_platform="${sc_platform}"
+              ;;
+          esac
+          
+          echo "Installing shellcheck ..."
+          wget -qO- "https://github.com/koalaman/shellcheck/releases/download/${sc_version?}/shellcheck-${sc_version?}.linux.${sc_platform}.tar.xz" \
+            | tar -xJv >/dev/null
+          sudo cp "shellcheck-${sc_version}/shellcheck" /usr/bin/
+          shellcheck --version
+
+          echo "Installing hadolint ..."
+          wget -q https://github.com/hadolint/hadolint/releases/download/${hl_version}/hadolint-Linux-${hl_platform}
+          sudo cp "hadolint-Linux-${hl_platform}" /usr/bin/hadolint
+          sudo chmod 755 /usr/bin/hadolint
+          hadolint --version
+
+      - name: Run quality checks
+        run: |
+          make -C build/containers checks
+
+  list:
+    name: List containers
+    runs-on: ubuntu-latest
+    env:
+      IS_TAG: ${{ startsWith(github.ref, 'refs/tags/') }}
+    outputs:
+      containers: ${{ steps.list-containers.outputs.containers }}
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 2
+
+      - id: list-containers
+        name: Determine containers
+        run: |
+          if [ "${IS_TAG}" == "false" ]; then
+            echo "Listing only the containers with changes"
+            containers=$( build/containers/build.sh --changed-containers-as-json)
+          elif [ "${IS_TAG}" == "true" ]; then
+            echo "Listing all the containers"
+            containers=$( build/containers/build.sh --all-containers-as-json)
+          fi
+          echo "containers = ${containers}"
+          echo "containers=${containers}" >> "$GITHUB_OUTPUT"
+
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+    needs:
+      - checks
+      - list
+    strategy:
+      max-parallel: 8
+      fail-fast: false
+      matrix:
+        container: ${{ fromJSON(needs.list.outputs.containers) }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Build Docker image
+        run: build/containers/build.sh --containers ${{ matrix.container }}
+
+  push:
+    name: Push
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    env:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+    needs:
+      - build
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Login to DockerHub
+        if: ${{ env.DOCKER_USERNAME != '' }}
+        run: echo ${{ secrets.DOCKER_PASSWORD }} | docker login -u ${{ secrets.DOCKER_USERNAME }} --password-stdin
+      
+      - name: Push Docker images
+        if: ${{ env.DOCKER_USERNAME != '' }}
+        run: |
+          build/containers/build.sh --dry-run --skip-build --push --all-containers
diff --git a/build/Makefile b/build/Makefile
index ca092b0e..b191e1ba 100644
--- a/build/Makefile
+++ b/build/Makefile
@@ -3,12 +3,10 @@ SHELL := /bin/bash
 .PHONY: all clean
 # trick to make all the first target
 # and set it to the end once all variables are defined
-all: containers datasets
+all: datasets
 
 build_dir = ..
 INTOGEN_DATASETS ?= ${build_dir}/datasets
-INTOGEN_CONTAINERS ?= ${build_dir}/containers
-
 
 # hg version
 genome = 38
@@ -17,17 +15,10 @@ cadd ?= 1.6
 # number of cores to use in steps that allow them
 cores ?= 1
 
-
 src_datasets = datasets
-src_containers = containers
-
-container_builder = ${src_containers}/build.sh
-
 
 # accumulate all targets
 DATASETS =
-CONTAINERS_SUDO =
-CONTAINERS_USER =
 
 # useful variables
 ensembl_db = "homo_sapiens_core_${ensembl}_${genome}"
@@ -39,9 +30,6 @@ grch = GRCh${genome}
 $(INTOGEN_DATASETS):
 	mkdir -p $@
 
-$(INTOGEN_CONTAINERS):
-	mkdir -p $@
-
 # Create checkpoints files so that if versions are changed
 # proper files are rebuild
 GENOME = $(INTOGEN_DATASETS)/.hg${genome}
@@ -55,23 +43,16 @@ $(ENSEMBL): | $(INTOGEN_DATASETS)
 $(CADD): | $(INTOGEN_DATASETS)
 	touch $@
 
-
-
 # Use second expansion for mixed dependencies
 .SECONDEXPANSION:
 
 include ${src_datasets}/*.mk
 include ${src_datasets}/*/*.mk
-include ${src_containers}/*/*.mk
 
 #########################
-.PHONY: datasets containers sudo
+.PHONY: datasets
 
 datasets: bgdata $(DATASETS) | $(INTOGEN_DATASETS)
 
-containers: $(CONTAINERS_USER) $(CONTAINERS_SUDO) | $(INTOGEN_CONTAINERS)
-
-sudo: $(CONTAINERS_SUDO) | $(INTOGEN_CONTAINERS)
-
 clean:
-	rm -rf $(INTOGEN_DATASETS) $(INTOGEN_CONTAINERS)
+	rm -rf $(INTOGEN_DATASETS)
diff --git a/build/containers/Makefile b/build/containers/Makefile
new file mode 100644
index 00000000..99ba101b
--- /dev/null
+++ b/build/containers/Makefile
@@ -0,0 +1,64 @@
+CURRENT_DIR := $(shell dirname $(abspath $(lastword $(MAKEFILE_LIST))))
+
+BUILD := $(CURRENT_DIR)/build.sh
+BUILD_ARGS ?=
+
+SHELLCHECK_BIN ?= shellcheck
+SHELLCHECK_ARGS ?= 
+
+HADOLINT_IGNORES := DL3059 # Multiple consecutive `RUN` instructions
+HADOLINT_IGNORES += DL3003 # Use WORKDIR to switch to a directory
+HADOLINT_IGNORES += DL3042 # Avoid use of cache directory with pip
+
+# HADOLINT_BIN := docker run --rm -i hadolint/hadolint hadolint
+HADOLINT_BIN ?= hadolint
+HADOLINT_ARGS ?= $(foreach ignore,$(HADOLINT_IGNORES),--ignore $(ignore))
+
+# Those ANSI codes are needed to print with colours
+GREEN := \033[0;32m
+WHITE := \033[0;37m
+BOLD := \033[1m
+BOLD_GREEN := $(GREEN)$(BOLD)
+BOLD_WHITE := $(WHITE)$(BOLD)
+RESET := \033[0m
+
+.DEFAULT_GOAL = checks
+
+.PHONY: checks
+checks: shellcheck hadolint
+
+.PHONY: shellcheck
+shellcheck:
+	@echo "$(BOLD_GREEN)Running cheks for shell scripts ...$(RESET)"
+	set -e; \
+	find -L $(CURRENT_DIR) -name '*.sh' | sed 's|$(CURRENT_DIR)/||' \
+		| while read -r script; do \
+		  echo "$(BOLD_WHITE)=> $${script}$(RESET)"; \
+		  $(SHELLCHECK_BIN) $(SHELLCHECK_ARGS) $${script}; \
+		  done
+
+.PHONY: hadolint
+hadolint:
+	@echo "$(BOLD_GREEN)Running checks for Dockerfile ...$(RESET)"
+	set -e; \
+	find -L $(CURRENT_DIR) -name 'Dockerfile' | sed 's|$(CURRENT_DIR)/||' \
+		| while read -r dockerfile; do \
+		  echo "$(BOLD_WHITE)=> $${dockerfile}$(RESET)"; \
+		  $(HADOLINT_BIN) $(HADOLINT_ARGS) - < $${dockerfile}; \
+		  done
+
+.PHONY: build-all
+build-all:
+	$(BUILD) --all-containers $(BUILD_ARGS)
+
+.PHONY: build-changes
+build-changes:
+	$(BUILD) $(BUILD_ARGS)
+
+.PHONY: push-all
+push-all:
+	$(BUILD) --push --all-containers $(BUILD_ARGS)
+
+.PHONY: push-changes
+push-changes:
+	$(BUILD) --push $(BUILD_ARGS)
diff --git a/build/containers/README.md b/build/containers/README.md
new file mode 100644
index 00000000..ec057779
--- /dev/null
+++ b/build/containers/README.md
@@ -0,0 +1,61 @@
+# Containers
+
+This folder contains all the containers needed by the intogen pipelines specifically.
+
+Every container will have an independent folder here or a link to another folder in the repository. Every of those folders need to include a `Dockerfile` with the specs to build the Docker image.
+
+## CI/CD
+
+The Github workflow `containers.yaml` will run the following jobs:
+- Run some quality checks to make sure that we follow the best practices
+- Determine which containers need to be built and/or pushed:
+    - When the push corresponds with a tag, all the containers will be built and pushed.
+    - When this is a regular push into a branch, only the containers that were modified will be built to make sure that they are not broken by the changes.
+
+You can run the workflow locally with the following command:
+
+```shell
+act -W '.github/workflows/containers.yaml'
+```
+
+Note that you will need to install the tool [act](https://github.com/nektos/act).
+
+## Local Development
+
+You can run the following commands (note that you can skip the `-C build/containers` argument if you run the commands from the `build/containers` folder):
+
+### Running quality checks
+
+We run two types of checks:
+- [shellcheck](https://github.com/koalaman/shellcheck) to make sure that bash scripts follow the best practices
+- [hadolint](https://github.com/hadolint/hadolint) to make sure that Dockerfiles follow the best practices
+
+You will need to install them in your computer before running the following commands:
+
+- To run both checks:
+
+    ```shell
+    make -C build/containers checks
+    ```
+
+- Or individually with:
+
+    ```shell
+    make -C build/containers shellcheck
+    ```
+
+    ```shell
+    make -C build/containers hadolint
+    ```
+
+### Building all the containers
+
+```shell
+make -C build/containers build-all
+```
+
+### Building only the containers that were modified
+
+```shell
+make -C build/containers build-changed
+```
diff --git a/build/containers/build.sh b/build/containers/build.sh
index 3f13d97e..4985818c 100755
--- a/build/containers/build.sh
+++ b/build/containers/build.sh
@@ -1,19 +1,196 @@
-#!/usr/bin/env bash
+#!/bin/bash
+
+# Automatically exit on any failure
 set -e
 
-FOLDER=$1
-IMAGE=$2
+# Those ANSI codes are needed to print with colours
+GREEN='\033[0;32m'
+YELLOW='\033[0;33m'
+CYAN='\033[0;36m'
+GREY='\033[38;5;241m'
+RED='\033[0;31m'
+# WHITE='\033[0;37m'
+BOLD='\033[1m'
+RESET='\033[0m' # Reset to default color
+
+# ---------------------------------------------------------------------------------------
+# Global variables ----------------------------------------------------------------------
+# ---------------------------------------------------------------------------------------
+
+# Set CONTAINERS_DIR to the path where this script is located
+CONTAINERS_DIR=$(readlink -f "${BASH_SOURCE[0]}" | xargs dirname)
+
+# List of containers (By default all folders with git changes)
+CONTAINERS=""
+
+# Whether to run or not docker comands
+DRY_RUN="false"
+
+# Whether to skip the build or not
+SKIP_BUILD="no"
+
+# Whether to push the containers into the DockerHub or not
+PUSH="false"
+
+# What docker binary to use
+DOCKER_BIN="docker"
+
+# BuildKit’s advanced features and output capabilities for the Docker builds
+export DOCKER_BUILDKIT=1
+export BUILDKIT_PROGRESS=plain
+
+# ---------------------------------------------------------------------------------------
+# Function to determine which containers have changes -----------------------------------
+# ---------------------------------------------------------------------------------------
+
+changed_containers() {
+	( git diff --cached --name-only && git diff --name-only HEAD~1 HEAD ) |
+        xargs dirname |
+        sed 's|^build/containers/||' | 
+        sed -E 's/^(combination|core)/intogen-\1/' |
+        sort -u |
+        while read -r path; do
+            if [ -f "${CONTAINERS_DIR}/$path/Dockerfile" ]; then
+                echo "$path"
+            fi
+        done
+}
+
+# ---------------------------------------------------------------------------------------
+# Function to determine all the containers available ------------------------------------
+# ---------------------------------------------------------------------------------------
+
+all_containers() {
+	find -L "${CONTAINERS_DIR}" -name 'Dockerfile' -print0 |
+		xargs -0 dirname | xargs basename | sort -u
+}
+
+# ---------------------------------------------------------------------------------------
+# Function to format a list of containers for display -----------------------------------
+# ---------------------------------------------------------------------------------------
+
+format_display() {
+	echo "$1" | tr '\n' ',' | sed -E 's/,$//'
+}
+
+# ---------------------------------------------------------------------------------------
+# Function to format a list of containers into JSON -------------------------------------
+# ---------------------------------------------------------------------------------------
+
+format_json() {
+	echo "$1" | jq --raw-input . | jq --slurp --compact-output .
+}
+
+# ---------------------------------------------------------------------------------------
+# Function to build the Docker images ---------------------------------------------------
+# ---------------------------------------------------------------------------------------
+
+# This will build each container sequentially.
+# It assumes that every container folder will contain a Dockerfile.
+# The Docker images will be named after its folder and tagged with the git tag.
+# Some folders are just symlinks to upper level folders.
+build() {
+	container=$1
+	tag=$2
+
+	image="${container}:${tag}"
+	echo -e "${GREEN}${BOLD}Building Docker image for ${YELLOW}${image}${GREEN} ...${RESET}"
+	command="${DOCKER_BIN} build -t ${image} ${CONTAINERS_DIR}/${container}"
+	echo -e "${GREY}> ${command}${RESET}"
+	if [ "${DRY_RUN}" != "yes" ]; then
+        eval "${command}"
+    fi
+}
+
+# ---------------------------------------------------------------------------------------
+# Function to push the containers to the DockerHub --------------------------------------
+# ---------------------------------------------------------------------------------------
+
+push() {
+	container=$1
+	tag=$2
+
+	image="${container}:${tag}"
+	echo -e "${GREEN}${BOLD}Pushing Docker image for ${YELLOW}${image}${GREEN} ...${RESET}"
+	command="${DOCKER_BIN} push ${image}"
+	echo -e "${GREY}> ${command}${RESET}"
+	if [ "${DRY_RUN}" != "yes" ]; then
+        eval "${command}"
+    fi
+}
+
+# ---------------------------------------------------------------------------------------
+# Parse command line arguments ----------------------------------------------------------
+# ---------------------------------------------------------------------------------------
+
+while [[ $# -gt 0 ]]; do
+	case $1 in
+	--changed-containers-as-json)
+		format_json "$(changed_containers)"
+		exit 0
+		;;
+	--all-containers-as-json)
+		format_json "$(all_containers)"
+		exit 0
+		;;
+	--containers)
+        CONTAINERS="${2//,/$'\n'}"
+		shift
+		shift
+		;;
+	--all-containers)
+		CONTAINERS=$(all_containers)
+		shift
+		;;
+	-n | --dry-run)
+		DRY_RUN="yes"
+		shift
+		;;
+	--skip-build)
+		SKIP_BUILD="yes"
+		shift
+		;;
+	--push)
+		PUSH="yes"
+		shift
+		;;
+	--podman)
+		DOCKER_BIN="podman"
+		shift
+		;;
+	*)
+		echo -e "${RED}${BOLD}Unknown option: ${YELLOW}$1${RESET}" >&2
+		exit 1
+		;;
+	esac
+done
+
+# ---------------------------------------------------------------------------------------
+# ---------------------------------------------------------------------------------------
+
+if [ -z "${CONTAINERS}" ]; then
+	CONTAINERS=$(changed_containers)
+fi
+
+CONTAINERS_FMT=$(format_display "$CONTAINERS")
+
+# Set TAG to either the current git tag name or else the git commit short SHA
+TAG=$(git describe --tags --exact-match 2>/dev/null || git rev-parse --short HEAD)
 
-tmpdir=`mktemp -d`
+echo -e "${CYAN}${BOLD}Containers: ${YELLOW}${CONTAINERS_FMT}${CYAN}${RESET}"
 
-## if you have root permission you can uncomment the following:
+if [ "${SKIP_BUILD}" == "no" ]; then
+	for container in ${CONTAINERS}; do
+		build "${container}" "${TAG}"
+	done
 
-# (cd ${FOLDER} && sudo singularity build ${tmpdir}/$(basename ${IMAGE}) Singularity)
-# mv ${tmpdir}/$(basename ${IMAGE}) ${IMAGE}
-# sudo chown ${USER}: ${IMAGE}
+	echo -e "${GREEN}${BOLD}All images built successfully for tag ${TAG}: ${YELLOW}${CONTAINERS_FMT}${CYAN}${RESET}"
+fi
 
-## if you DO NOT have root permission then you could use the --fakeroot flag as long as your user is specified in the /etc/subuid and /etc/subgid files. See https://docs.sylabs.io/guides/3.6/admin-guide/user_namespace.html#user-namespaces-fakeroot for more info. 
+if [ "${PUSH}" == "yes" ]; then
+	for container in ${CONTAINERS}; do
+		push "${container}" "${TAG}"
+	done
 
-(cd ${FOLDER} && singularity build --fakeroot ${tmpdir}/$(basename ${IMAGE}) Singularity)
-mv ${tmpdir}/$(basename ${IMAGE}) ${IMAGE}
-chown ${USER}: ${IMAGE}
+	echo -e "${GREEN}${BOLD}All images pushed successfully for tag ${TAG}: ${YELLOW}${CONTAINERS_FMT}${CYAN}${RESET}"
+fi
diff --git a/build/containers/cbase/Singularity b/build/containers/cbase/Singularity
deleted file mode 100644
index 303b9a90..00000000
--- a/build/containers/cbase/Singularity
+++ /dev/null
@@ -1,19 +0,0 @@
-Bootstrap: docker
-From: debian:buster-slim
-
-%environment
-    export LC_ALL=C.UTF-8
-
-%runscript
-    exec "/usr/bin/python" "/cbase/cbase.py" "$@"
-
-%setup
-    mkdir ${SINGULARITY_ROOTFS}/cbase
-    cp cbase.py ${SINGULARITY_ROOTFS}/cbase/cbase.py
-    cp -r Auxiliary/ ${SINGULARITY_ROOTFS}/cbase/Auxiliary/
-    chmod -R a+xr ${SINGULARITY_ROOTFS}/cbase/
-
-%post
-    apt-get update
-    apt-get install -y python-scipy python-statsmodels python-mpmath
-    rm -rf /var/lib/apt/lists/*
diff --git a/build/containers/cbase/cbase.mk b/build/containers/cbase/cbase.mk
deleted file mode 100644
index 355364fa..00000000
--- a/build/containers/cbase/cbase.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-
-CBASE_CONTAINER = $(INTOGEN_CONTAINERS)/cbase.simg
-
-cbase_container_srcdir = ${src_containers}/cbase
-
-cbase_container_src = ${cbase_container_srcdir}/cbase.py \
-	${cbase_container_srcdir}/Singularity
-
-$(CBASE_CONTAINER): $(cbase_container_src) | $(INTOGEN_CONTAINERS)
-	@echo Building CBaSE container
-	${container_builder} ${cbase_container_srcdir} $@
-
-
-CONTAINERS_SUDO += $(CBASE_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/combination/Singularity b/build/containers/combination/Singularity
deleted file mode 100644
index de1150a5..00000000
--- a/build/containers/combination/Singularity
+++ /dev/null
@@ -1,16 +0,0 @@
-Bootstrap: docker
-From: python:3.9
-
-%environment
-
-%runscript
-
-%setup
-	cp -r ../../../combination ${SINGULARITY_ROOTFS}/combination/
-
-%post
-
-	pip install /combination
-
-    # Clean unused things
-    rm -rf /var/lib/apt/lists/*
diff --git a/build/containers/combination/combination.mk b/build/containers/combination/combination.mk
deleted file mode 100644
index d42b9a7c..00000000
--- a/build/containers/combination/combination.mk
+++ /dev/null
@@ -1,17 +0,0 @@
-
-COMBINATION_CONTAINER = $(INTOGEN_CONTAINERS)/intogen-combination.simg
-
-combination_container_srcdir = ${src_containers}/combination
-
-combination_code_folder = ${src_containers}/../../combination
-
-combination_container_src = ${combination_container_srcdir}/Singularity \
-	${combination_code_folder}/setup.py \
-	$(wildcard ${combination_code_folder}/intogen_combination/*) \
-	$(wildcard ${combination_code_folder}/*)
-
-$(COMBINATION_CONTAINER): ${combination_container_src} | $(INTOGEN_CONTAINERS)
-	@echo Building combination container
-	${container_builder} ${combination_container_srcdir} $@
-
-CONTAINERS_SUDO += $(COMBINATION_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/core/Singularity b/build/containers/core/Singularity
deleted file mode 100644
index d1199dde..00000000
--- a/build/containers/core/Singularity
+++ /dev/null
@@ -1,23 +0,0 @@
-Bootstrap: docker
-From: python:3
-
-%environment
-    export LC_ALL=C.UTF-8
-
-%runscript
-
-%setup
-	cp -r ../../../core ${SINGULARITY_ROOTFS}/core/
-	cp get_field.sh ${SINGULARITY_ROOTFS}/usr/local/bin/get_field.sh
-	chmod a+rx ${SINGULARITY_ROOTFS}/usr/local/bin/get_field.sh
-    chmod -R a+rx ${SINGULARITY_ROOTFS}/core/
-
-%post
-	# Install openVariant
-    pip install open-variant
-    
-    # Install intogen-core package
-	pip install /core
-
-    # Clean unused things
-    rm -rf /var/lib/apt/lists/*
diff --git a/build/containers/core/core.mk b/build/containers/core/core.mk
deleted file mode 100644
index 1454db37..00000000
--- a/build/containers/core/core.mk
+++ /dev/null
@@ -1,19 +0,0 @@
-
-CORE_CONTAINER = $(INTOGEN_CONTAINERS)/intogen-core.simg
-
-core_container_srcdir = ${src_containers}/core
-
-core_code_folder = ${src_containers}/../../core
-
-core_container_src = ${core_container_srcdir}/Singularity \
-	${core_container_srcdir}/get_field.sh \
-	${core_code_folder}/setup.py \
-	$(wildcard ${core_code_folder}/intogen_core/*.py) \
-	$(wildcard ${core_code_folder}/intogen_core/*/*.py) \
-	$(wildcard ${core_code_folder}/intogen_core/*/*/*.py)
-
-$(CORE_CONTAINER): ${core_container_src} | $(INTOGEN_CONTAINERS)
-	@echo Building core container
-	${container_builder} ${core_container_srcdir} $@
-
-CONTAINERS_SUDO += $(CORE_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/core/get_field.sh b/build/containers/core/get_field.sh
deleted file mode 100755
index 5df9d95b..00000000
--- a/build/containers/core/get_field.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env bash
-set -e
-
-input=$1
-field=$2
-
-C=1
-header=`zcat ${input} | head -n 1`
-for i in ${header}
-do
-	if [[ $i == "${field}" ]]
-	then
-		break
-	else
-		C=$(( $C + 1 ))
-	fi
-done
-
-zcat ${input} | sed -n '2p' | cut -f$C | xargs printf
\ No newline at end of file
diff --git a/build/containers/deconstructsig/Singularity b/build/containers/deconstructsig/Singularity
deleted file mode 100644
index 2caeb385..00000000
--- a/build/containers/deconstructsig/Singularity
+++ /dev/null
@@ -1,25 +0,0 @@
-Bootstrap: docker
-From: debian:buster-slim
-
-%environment
-    export LC_ALL=C.UTF-8
-    
-%runscript
-    exec "/usr/bin/python3" "/deconstructsig/run_deconstruct.py" "$@"
-
-%setup
-    mkdir ${SINGULARITY_ROOTFS}/deconstructsig
-    cp run_deconstruct.py ${SINGULARITY_ROOTFS}/deconstructsig/
-    cp deconstructSigs.r ${SINGULARITY_ROOTFS}/deconstructsig/
-    cp signature_assignment.py ${SINGULARITY_ROOTFS}/deconstructsig/
-    cp output_pass_drivers_01.csv ${SINGULARITY_ROOTFS}/deconstructsig/
-    chmod -R a+rx ${SINGULARITY_ROOTFS}/deconstructsig/
-
-%post
-    apt-get update
-    apt-get install -y python3-pandas python3-click r-bioc-bsgenome r-cran-gplots procps
-    rm -rf /var/lib/apt/lists/*
-    echo "install.packages(\"BiocManager\", repos=\"https://cran.r-project.org\")" | R --no-save
-    echo "BiocManager::install(\"BSgenome.Hsapiens.UCSC.hg19\")" | R --no-save
-    echo "BiocManager::install(\"BSgenome.Hsapiens.UCSC.hg38\")" | R --no-save
-    echo "install.packages(\"deconstructSigs\", repos=\"https://cran.r-project.org\")" | R --no-save
diff --git a/build/containers/deconstructsig/deconstructsigs.mk b/build/containers/deconstructsig/deconstructsigs.mk
deleted file mode 100644
index 9e023a93..00000000
--- a/build/containers/deconstructsig/deconstructsigs.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-
-DECONSTRUCTSIGS_CONTAINER = $(INTOGEN_CONTAINERS)/deconstructsigs.simg
-
-deconstructsigs_container_srcdir = ${src_containers}/deconstructsig
-
-deconstructsigs_container_src = $(wildcard ${deconstructsigs_container_srcdir}/*)
-
-$(DECONSTRUCTSIGS_CONTAINER): $(deconstructsigs_container_src) | $(INTOGEN_CONTAINERS)
-	@echo Building deconstructSigs container
-	${container_builder} ${deconstructsigs_container_srcdir} $@
-
-CONTAINERS_SUDO += $(DECONSTRUCTSIGS_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/dndscv/Singularity b/build/containers/dndscv/Singularity
deleted file mode 100644
index 882c1498..00000000
--- a/build/containers/dndscv/Singularity
+++ /dev/null
@@ -1,22 +0,0 @@
-Bootstrap: docker
-From: debian:buster-slim
-
-%environment
-    export LC_ALL=C.UTF-8
-    
-%runscript
-    exec "Rscript" "/dndscv/dndscv.R" "$@"
-
-%setup
-    mkdir ${SINGULARITY_ROOTFS}/dndscv
-    cp dndscv.R ${SINGULARITY_ROOTFS}/dndscv/
-    cp dndscv.tar.gz ${SINGULARITY_ROOTFS}/dndscv/
-    chmod -R a+rx ${SINGULARITY_ROOTFS}/dndscv/
-
-%post
-    apt-get update
-    apt-get -y install locales-all r-base r-cran-devtools r-bioc-biostrings r-bioc-genomicranges r-bioc-rsamtools r-cran-ade4 r-cran-seqinr procps
-    rm -rf /var/lib/apt/lists/*
-    # echo "library(devtools); install_github('im3sanger/dndscv')" | R --no-save
-    echo "library(devtools)" | R --no-save
-    R CMD INSTALL "/dndscv/dndscv.tar.gz"
diff --git a/build/containers/dndscv/dndscv.mk b/build/containers/dndscv/dndscv.mk
deleted file mode 100644
index bd38d28e..00000000
--- a/build/containers/dndscv/dndscv.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-
-DNDSCV_CONTAINER = $(INTOGEN_CONTAINERS)/dndscv.simg
-
-dndscv_container_srcdir = ${src_containers}/dndscv
-
-dndscv_container_src = ${dndscv_container_srcdir}/dndscv.R \
-	${dndscv_container_srcdir}/dndscv.tar.gz \
-	${dndscv_container_srcdir}/Singularity
-
-$(DNDSCV_CONTAINER): $(dndscv_container_src) | $(INTOGEN_CONTAINERS)
-	@echo Building dNdScv container
-	${container_builder} ${dndscv_container_srcdir} $@
-
-CONTAINERS_SUDO += $(DNDSCV_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/dndscv/dndscv.tar.gz b/build/containers/dndscv/dndscv.tar.gz
deleted file mode 100644
index 1225dd9e..00000000
--- a/build/containers/dndscv/dndscv.tar.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:c00bfd80ace2a1d5e38afa4031131ea44eecce9bb83f5502f0085dd2fe560db1
-size 114417210
diff --git a/build/containers/dndscv/dndscv.tar.gz.REMOVED.git-id b/build/containers/dndscv/dndscv.tar.gz.REMOVED.git-id
deleted file mode 100644
index 7801ab9d..00000000
--- a/build/containers/dndscv/dndscv.tar.gz.REMOVED.git-id
+++ /dev/null
@@ -1 +0,0 @@
-ef1e05dfea6c66e5735c740499a5d9c5ed2990a6
\ No newline at end of file
diff --git a/build/containers/hotmaps/Singularity b/build/containers/hotmaps/Singularity
deleted file mode 100644
index 81090667..00000000
--- a/build/containers/hotmaps/Singularity
+++ /dev/null
@@ -1,19 +0,0 @@
-Bootstrap: docker
-From: alpine:3.8
-
-%environment
-    export LC_ALL=C.UTF-8
-    
-%runscript
-    exec "/bin/sh" "/hotmaps/hotmaps.sh" "$@"
-
-%setup
-    mkdir ${SINGULARITY_ROOTFS}/hotmaps
-    cp -r scripts ${SINGULARITY_ROOTFS}/hotmaps/
-    cp hotmaps.sh ${SINGULARITY_ROOTFS}/hotmaps/
-    chmod -R a+r,a+x ${SINGULARITY_ROOTFS}/hotmaps/
-
-%post
-    apk add --no-cache python-dev py-pip py-curl zlib-dev make ncurses-dev g++ bash procps
-    pip --no-cache-dir install numpy==1.16.5 
-    pip --no-cache-dir install pandas==0.24.2 tqdm futures bgreference biopython==1.76 pyliftover
diff --git a/build/containers/hotmaps/hotmaps.mk b/build/containers/hotmaps/hotmaps.mk
deleted file mode 100644
index 588ab917..00000000
--- a/build/containers/hotmaps/hotmaps.mk
+++ /dev/null
@@ -1,13 +0,0 @@
-
-HOTMAPS_CONTAINER = $(INTOGEN_CONTAINERS)/hotmaps.simg
-
-hotmaps_container_srcdir = ${src_containers}/hotmaps
-
-hotmaps_container_src = $(wildcard ${hotmaps_container_srcdir}/*) \
-	${hotmaps_container_srcdir}/hotmaps.sh ${hotmaps_container_srcdir}/Singularity
-
-$(HOTMAPS_CONTAINER): $(hotmaps_container_src) | $(INTOGEN_CONTAINERS)
-	@echo Building HotMAPS container
-	${container_builder} ${hotmaps_container_srcdir} $@
-
-CONTAINERS_SUDO += $(HOTMAPS_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/hotmaps/hotmaps.sh b/build/containers/hotmaps/hotmaps.sh
deleted file mode 100755
index 62577e52..00000000
--- a/build/containers/hotmaps/hotmaps.sh
+++ /dev/null
@@ -1,137 +0,0 @@
-#!/bin/sh
-set -x
-
-# Script arguments
-INPUT_FILE=$1
-OUTPUT_FOLDER=$2
-SIGNATURE_FILE=$3
-DATA_FOLDER=$4
-CORES=$5
-
-# Enviroment variables
-HYPERMUT=1000
-SCRIPTS_FOLDER="/hotmaps/scripts"
-
-DATASETS_FOLDER=$INTOGEN_DATASETS/hotmaps
-
-    
-# Preprocess
-input_folder=$(dirname "${INPUT_FILE}")
-input_name=$(basename "${INPUT_FILE}")
-name=${input_name%.in.maf}
-
-TEMP_FOLDER="$OUTPUT_FOLDER/${name}.tmp"
-mkdir -p $TEMP_FOLDER
-
-input_filename=${name}.maf
-cp ${INPUT_FILE} ${TEMP_FOLDER}/${input_filename}
-
-
-# TODO remove the file checks
-
-## STEP1. Map to Structure (output: non_filtered_mupit.INPUT_FILENAME)
-if [ ! -f "$TEMP_FOLDER/non_filtered_mupit.${input_filename}" ]
-then
-    python $SCRIPTS_FOLDER/map_maf_to_structure.py \
-        --data-dir ${TEMP_FOLDER} \
-        --match-regex ${input_filename} \
-        --output-dir $TEMP_FOLDER \
-        --database ${DATA_FOLDER}/mupit_database.db
-    rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi
-fi
-
-## STEP2. Convert MAF to MUPIT (output: coverage_info.txt, INPUT_FILENAME.mupit )
-if [ ! -f "$TEMP_FOLDER/${input_filename}.mupit" ]
-then
-    python $SCRIPTS_FOLDER/convert_maf_to_mupit.py \
-        --maf ${TEMP_FOLDER}/${input_filename} \
-        --tumor-type ${name} \
-        --no-stratify \
-        -mt $HYPERMUT \
-        -i $TEMP_FOLDER \
-        --output $TEMP_FOLDER/${input_filename}.mupit \
-        --database ${DATA_FOLDER}/mupit_database.db
-    rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi
-fi
-
-## STEP3. Filter hypermutated (output: mupit.INPUT_FILENAME)
-if [ ! -f "$TEMP_FOLDER/mupit.${input_filename}" ]
-then
-    python $SCRIPTS_FOLDER/filter_hypermutated.py \
-        --raw-dir $TEMP_FOLDER \
-        --match-regex ${input_filename} \
-        --mut-threshold $HYPERMUT \
-        --sample-col 'Tumor_Sample_Barcode' \
-        --data-dir $TEMP_FOLDER
-    rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi
-fi
-
-## STEP4. Count mutations (input: mupit.* output: collected.INPUT_FILENAME)
-if [ ! -f "$TEMP_FOLDER/collected.${input_filename}" ]
-then
-    python $SCRIPTS_FOLDER/count_mutations.py \
-        --data-dir $TEMP_FOLDER
-    rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi
-fi
-
-## STEP5. Format mutations table (input: collected.* output: mutation_tcga.INPUT_FILENAME.txt)
-if [ ! -f "$TEMP_FOLDER/mutation_tcga.${input_filename}" ]
-then
-    python $SCRIPTS_FOLDER/format_mutations_table.py \
-    	--data-dir $TEMP_FOLDER
-    rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi
-fi
-
-## STEP7. Run HotMAPS (input: mutation_tcga.NAME.txt output:hotspot_INPUT_FILENAME)
-if [ ! -f "$TEMP_FOLDER/hotspot_${input_filename}" ]
-then
-    python $SCRIPTS_FOLDER/hotspot.py \
-        --log-level=INFO \
-        -m $TEMP_FOLDER/mutation_tcga.${name}.txt \
-        -a ${DATA_FOLDER}/fully_described_pdb_info.txt \
-        -t EVERY -n 10000 -r 10.0 -c $CORES \
-        -o $TEMP_FOLDER/hotspot_${input_filename} \
-        -e $TEMP_FOLDER/${input_filename}.err --log=stdout \
-        -gc $DATASETS_FOLDER/coordinates.txt.gz \
-        -S $SIGNATURE_FILE \
-        --maf ${TEMP_FOLDER}/${input_filename} \
-        --database ${DATA_FOLDER}/mupit_database.db \
-        --pdb ${DATA_FOLDER}/pdb
-    rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi
-fi
-
-## STEP8. Multiple test
-if [ ! -f "$TEMP_FOLDER/mtco_${input_filename}" ]
-then
-    python $SCRIPTS_FOLDER/multiple_testing_correction.py \
-        -i $TEMP_FOLDER/hotspot_${input_filename} \
-        -f min -q 0.05 \
-        -m $TEMP_FOLDER/${input_filename}.mupit \
-        -o $TEMP_FOLDER/mtco_${input_filename} \
-        -s $TEMP_FOLDER/mtcs_${input_filename}
-    rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi
-fi
-
-## STEP9. Find Hotspots regions gene
-if [ ! -f "$TEMP_FOLDER/hotspot_gene_${input_filename}" ]
-then
-    python $SCRIPTS_FOLDER/find_hotspot_regions_gene.py \
-        -m $TEMP_FOLDER/mtco_${input_filename} \
-        -a $TEMP_FOLDER/${input_filename}.mupit \
-        -p ${DATA_FOLDER}/fully_described_pdb_info.txt \
-        -r 10.0 -q 0.05 \
-        -o $TEMP_FOLDER/hotspot_gene_${input_filename} \
-        --pdb ${DATA_FOLDER}/pdb
-    rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi
-fi
-
-## STEP10. Output parser
-if [ ! -f "$OUTPUT_FOLDER/${name}.out.gz" ]
-then
-    python ${SCRIPTS_FOLDER}/postprocess.py \
-    	${TEMP_FOLDER}/hotspot_gene_${input_filename} \
-    	${TEMP_FOLDER}/mtco_${input_filename} \
-    	${OUTPUT_FOLDER}/${name}.out.gz \
-    	$OUTPUT_FOLDER/${name}.clusters.gz
-    rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi
-fi
\ No newline at end of file
diff --git a/build/containers/cbase/Auxiliary/CBaSE_v1.1_parameters.py b/build/containers/intogen-cbase/Auxiliary/CBaSE_v1.1_parameters.py
similarity index 100%
rename from build/containers/cbase/Auxiliary/CBaSE_v1.1_parameters.py
rename to build/containers/intogen-cbase/Auxiliary/CBaSE_v1.1_parameters.py
diff --git a/build/containers/cbase/Auxiliary/CBaSE_v1.1_qvalues.py b/build/containers/intogen-cbase/Auxiliary/CBaSE_v1.1_qvalues.py
similarity index 100%
rename from build/containers/cbase/Auxiliary/CBaSE_v1.1_qvalues.py
rename to build/containers/intogen-cbase/Auxiliary/CBaSE_v1.1_qvalues.py
diff --git a/build/containers/intogen-cbase/Dockerfile b/build/containers/intogen-cbase/Dockerfile
new file mode 100644
index 00000000..497eec0f
--- /dev/null
+++ b/build/containers/intogen-cbase/Dockerfile
@@ -0,0 +1,20 @@
+FROM debian:buster-slim
+
+ENV LC_ALL=C.UTF-8
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends --no-install-suggests \
+        python2.7=2.7.16-2+deb10u4 \
+        python-scipy=1.1.0-7 \
+        python-statsmodels=0.8.0-9 \
+        python-mpmath=1.1.0-1 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN --mount=type=bind,target=/files \
+    mkdir -p /cbase && \
+    cp -a /files/Auxiliary /cbase/ && \
+    cp /files/cbase.py /cbase/ && \
+    chmod -R a+xr /cbase
+
+ENTRYPOINT ["/usr/bin/python", "/cbase/cbase.py"]
diff --git a/build/containers/cbase/cbase.py b/build/containers/intogen-cbase/cbase.py
similarity index 100%
rename from build/containers/cbase/cbase.py
rename to build/containers/intogen-cbase/cbase.py
diff --git a/build/containers/intogen-combination b/build/containers/intogen-combination
new file mode 120000
index 00000000..26b8d221
--- /dev/null
+++ b/build/containers/intogen-combination
@@ -0,0 +1 @@
+../../combination
\ No newline at end of file
diff --git a/build/containers/intogen-core b/build/containers/intogen-core
new file mode 120000
index 00000000..3d25ddeb
--- /dev/null
+++ b/build/containers/intogen-core
@@ -0,0 +1 @@
+../../core
\ No newline at end of file
diff --git a/build/containers/intogen-deconstructsig/Dockerfile b/build/containers/intogen-deconstructsig/Dockerfile
new file mode 100644
index 00000000..fad9d38f
--- /dev/null
+++ b/build/containers/intogen-deconstructsig/Dockerfile
@@ -0,0 +1,36 @@
+FROM debian:buster-slim
+
+ENV LC_ALL=C.UTF-8
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends --no-install-suggests \
+        python3.7-minimal=3.7.3-2+deb10u7 \
+        python3-pandas=0.23.3+dfsg-3 \
+        python3-click=7.0-1 \
+        r-bioc-bsgenome=1.50.0-1 \
+        r-cran-gplots=3.0.1.1-1 \
+        procps=2:3.3.15-2 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN R --vanilla <<EOF
+tryCatch(
+{
+    install.packages("BiocManager", repos="https://cran.r-project.org")
+    BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
+    BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
+    install.packages("https://cran.r-project.org/src/contrib/Archive/deconstructSigs/deconstructSigs_1.8.0.tar.gz", repos=NULL, type="source")
+}, error = function(e) {
+    cat('Error:', e$message, '\n')
+    quit(status = 1)
+})
+EOF
+
+RUN --mount=type=bind,target=/files \
+    mkdir -p /deconstructsig && \
+    cd /files && \
+    cp run_deconstruct.py deconstructSigs.r signature_assignment.py /deconstructsig/ && \
+    chmod -R a+rx /deconstructsig/ && \
+    cp output_pass_drivers_01.csv /deconstructsig/
+
+ENTRYPOINT [ "/usr/bin/python3", "/deconstructsig/run_deconstruct.py" ]
diff --git a/build/containers/deconstructsig/deconstructSigs.r b/build/containers/intogen-deconstructsig/deconstructSigs.r
similarity index 100%
rename from build/containers/deconstructsig/deconstructSigs.r
rename to build/containers/intogen-deconstructsig/deconstructSigs.r
diff --git a/build/containers/deconstructsig/output_pass_drivers_01.csv b/build/containers/intogen-deconstructsig/output_pass_drivers_01.csv
similarity index 100%
rename from build/containers/deconstructsig/output_pass_drivers_01.csv
rename to build/containers/intogen-deconstructsig/output_pass_drivers_01.csv
diff --git a/build/containers/deconstructsig/run_deconstruct.py b/build/containers/intogen-deconstructsig/run_deconstruct.py
similarity index 100%
rename from build/containers/deconstructsig/run_deconstruct.py
rename to build/containers/intogen-deconstructsig/run_deconstruct.py
diff --git a/build/containers/deconstructsig/signature_assignment.py b/build/containers/intogen-deconstructsig/signature_assignment.py
similarity index 100%
rename from build/containers/deconstructsig/signature_assignment.py
rename to build/containers/intogen-deconstructsig/signature_assignment.py
diff --git a/build/containers/intogen-dndscv/Dockerfile b/build/containers/intogen-dndscv/Dockerfile
new file mode 100644
index 00000000..08479bcd
--- /dev/null
+++ b/build/containers/intogen-dndscv/Dockerfile
@@ -0,0 +1,59 @@
+FROM debian:buster-slim AS build
+
+ENV LC_ALL=C.UTF-8
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get -y install --no-install-recommends --no-install-suggests \
+        ca-certificates=20200601~deb10u2 \
+        git=1:2.20.1-2+deb10u9 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN --mount=type=bind,target=/files \
+    git config --global http.postBuffer 524288000 && \
+    git config --global http.lowSpeedLimit 0 && \
+    git config --global http.lowSpeedTime 999999 && \
+    git config --global http.retry 5 && \
+    git clone --filter=blob:none https://github.com/im3sanger/dndscv.git && \
+    cd dndscv && \
+    git checkout ac3437e6c5299617e044b62243c0bea8a242ae54 && \
+    git fetch --depth 1 && \
+    cp /files/dndscv.patch / && \
+    git apply /dndscv.patch && \
+    cd .. && \
+    tar --exclude='.git' -cvzf dndscv.tar.gz dndscv
+
+FROM debian:buster-slim AS final
+
+ENV LC_ALL=C.UTF-8
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get -y install --no-install-recommends --no-install-suggests \
+        locales-all=2.28-10+deb10u4 \
+        r-base=3.5.2-1 \
+        r-cran-devtools=2.0.1-1 \
+        r-cran-ade4=1.7-13-1 \
+        r-cran-seqinr=3.4-5-2+b1 \
+        r-bioc-biostrings=2.50.2-1 \
+        r-bioc-genomicranges=1.34.0+dfsg-1 \
+        r-bioc-rsamtools=1.34.1-1 \
+        procps=2:3.3.15-2 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN --mount=type=bind,from=build,target=/build R --vanilla <<EOF
+tryCatch(
+{
+    library(devtools)
+    install.packages("/build/dndscv.tar.gz", repos=NULL, type="source")
+}, error = function(e) {
+    cat('Error:', e$message, '\n')
+    quit(status = 1)
+})
+EOF
+
+RUN --mount=type=bind,target=/files \
+    mkdir -p /dndscv && \
+    cp /files/dndscv.R /dndscv/
+
+ENTRYPOINT [ "Rscript", "/dndscv/dndscv.R" ]
diff --git a/build/containers/dndscv/dndscv.R b/build/containers/intogen-dndscv/dndscv.R
similarity index 100%
rename from build/containers/dndscv/dndscv.R
rename to build/containers/intogen-dndscv/dndscv.R
diff --git a/build/containers/intogen-dndscv/dndscv.patch b/build/containers/intogen-dndscv/dndscv.patch
new file mode 100644
index 00000000..44ae907a
--- /dev/null
+++ b/build/containers/intogen-dndscv/dndscv.patch
@@ -0,0 +1,168 @@
+diff --git a/INSTRUCTIONS.loris b/INSTRUCTIONS.loris
+new file mode 100644
+index 0000000..2a1258d
+--- /dev/null
++++ b/INSTRUCTIONS.loris
+@@ -0,0 +1,32 @@
++# Create a dndscv package
++rm dndscv.tar.gz
++tar cvzf dndscv.tar.gz dndscv/
++R CMD INSTALL dndscv.tar.gz
++
++
++# How to run
++$  source activate dndscv
++$  export INTOGEN_DATASETS="/workspace/projects/intogen_2017/pipeline/datasets/hg38_vep92_develop/"
++
++$  R
++
++>>> library("dndscv")
++>>> muts = read.table(gzfile("/workspace/projects/intogen_2017/runs/20190220/work/2d/9b30aa1d8a871b00fc11169696744a/dndscv/TARGET_WGS_WT_US.in.gz"), sep = '\t', header = TRUE)
++>>> dndscv(muts, refdb=file.path(Sys.getenv("INTOGEN_DATASETS"), "dndscv", "RefCDS.rda"))
++
++
++
++writeOutput = 0
++tryCatch({
++    result <- dndscv(muts, refdb=file.path(Sys.getenv("INTOGEN_DATASETS"), "dndscv", "RefCDS.rda"))
++    writeOutput <- 1
++}, error=function(e) {
++    message('dndsCV raised an error')
++    writeOutput <- 2
++})
++
++
++
++write.table(result$sel_cv, gzfile(args[2]), quote=FALSE, sep='\t', row.names = FALSE)
++write.table(result$annotmuts, gzfile(args[3]), sep = "\t", quote = FALSE, row.names = FALSE)
++write.table(result$genemuts, gzfile(args[4]), sep = "\t", quote = FALSE, row.names = FALSE)
+diff --git a/R/dndscv.R b/R/dndscv.R
+index 8c86403..fe3cdb7 100755
+--- a/R/dndscv.R
++++ b/R/dndscv.R
+@@ -399,6 +399,10 @@ dndscv = function(mutations, gene_list = NULL, refdb = "hg19", sm = "192r_3w", k
+     if (outp > 2) {
+         
+         message("[5] Running dNdScv...")
++
++        if (sum(genemuts$n_syn) < 5) {
++            stop('Less then 5 synonymous mutations')
++        }
+     
+         # Covariates
+         if (is.null(cv)) {
+@@ -412,17 +416,26 @@ dndscv = function(mutations, gene_list = NULL, refdb = "hg19", sm = "192r_3w", k
+                 covs = covs[,1:maxcovs]
+             }
+             nbrdf = cbind(genemuts[,c("n_syn","exp_syn")], covs)
+-            
++
+             # Negative binomial regression for substitutions
+             if (nrow(genemuts)<500) { # If there are <500 genes, we run the regression without covariates
+                 model = MASS::glm.nb(n_syn ~ offset(log(exp_syn)) - 1 , data = nbrdf)
+             } else {
+                 model = tryCatch({
++                    message('--normal')
+                     MASS::glm.nb(n_syn ~ offset(log(exp_syn)) + . , data = nbrdf) # We try running the model with covariates
+                 }, warning = function(w){
++                    message('--warning')
+                     MASS::glm.nb(n_syn ~ offset(log(exp_syn)) - 1 , data = nbrdf) # If there are warnings or errors we run the model without covariates
+                 }, error = function(e){
++                    message('--error')
+                     MASS::glm.nb(n_syn ~ offset(log(exp_syn)) - 1 , data = nbrdf) # If there are warnings or errors we run the model without covariates
++
++                    # tryCatch({
++                    #     MASS::glm.nb(n_syn ~ offset(log(exp_syn)) - 1 , data = nbrdf) # If there are warnings or errors we run the model without covariates
++                    # }, error = function(e){
++                    #     stop('MASS::gml.nb ERROR')
++                    # })
+                 })
+             }
+             message(sprintf("    Regression model for substitutions (theta = %0.3g).", model$theta))
+diff --git a/run_dndscv.R b/run_dndscv.R
+new file mode 100644
+index 0000000..94c61c7
+--- /dev/null
++++ b/run_dndscv.R
+@@ -0,0 +1,81 @@
++
++library("dndscv")
++
++muts = read.table(gzfile('/workspace/projects/intogen_2017/runs/20190124/dndscv/CBIOP_WXS_MDS_TOKYO_2011.in.gz'), sep = '\t', header = TRUE)
++
++writeOutput = 0
++result = tryCatch({
++    dndscv(muts, refdb="/workspace/projects/intogen_2017/pipeline/datasets/hg38_vep92_develop/dndscv/RefCDS.rda")
++    writeOutput = 1
++}, error=function(e) {
++    message('There was an error')
++    writeOutput = 2
++})
++
++if (writeOutput == 1) {
++    write.table(result$sel_cv, 'file1.txt', quote=FALSE, sep='\t', row.names = FALSE)
++    write.table(result$annotmuts, 'file2.txt', sep = "\t", quote = FALSE, row.names = FALSE)
++    write.table(result$genemuts, 'file3.txt', sep = "\t", quote = FALSE, row.names = FALSE)
++} else {
++    df = data.frame(
++        gene_name=character(),
++        n_syn=character(),
++        n_mis=character(),
++        n_non=character(),
++        n_spl=character(),
++        n_ind=character(),
++        wmis_cv=character(),
++        wnon_cv=character(),
++        wspl_cv=character(),
++        wind_cv=character(),
++        pmis_cv=character(),
++        ptrunc_cv=character(),
++        pallsubs_cv=character(),
++        pind_cv=character(),
++        qmis_cv=character(),
++        qtrunc_cv=character(),
++        qallsubs_cv=character(),
++        pglobal_cv=character(),
++        qglobal_cv=character(),
++	stringsAsFactors=FALSE
++    )
++    write.table(df, 'file1.txt', sep = "\t", quote = FALSE, row.names = FALSE)
++
++    df = data.frame(
++        sampleID=character(),
++        chr=character(),
++        pos=character(),
++        ref=character(),
++        mut=character(),
++        gene=character(),
++        strand=character(),
++        ref_cod=character(),
++        mut_cod=character(),
++        ref3_cod=character(),
++        mut3_cod=character(),
++        aachange=character(),
++        ntchange=character(),
++        codonsub=character(),
++        impact=character(),
++        pid=character(),
++	stringsAsFactors=FALSE
++    )
++    write.table(df, 'file2.txt', sep = "\t", quote = FALSE, row.names = FALSE)
++
++    df = data.frame(
++        gene_name=character(),
++        n_syn=character(),
++        n_mis=character(),
++        n_non=character(),
++        n_spl=character(),
++        exp_syn=character(),
++        exp_mis=character(),
++        exp_non=character(),
++        exp_spl=character(),
++        exp_syn_cv=character(),
++	stringsAsFactors=FALSE
++    )
++    write.table(df, 'file3.txt', sep = "\t", quote = FALSE, row.names = FALSE)
++}
++
++
diff --git a/build/containers/intogen-hotmaps/Dockerfile b/build/containers/intogen-hotmaps/Dockerfile
new file mode 100644
index 00000000..c495969c
--- /dev/null
+++ b/build/containers/intogen-hotmaps/Dockerfile
@@ -0,0 +1,26 @@
+FROM alpine:3.8
+
+ENV LC_ALL=C.UTF-8
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apk add --no-cache \
+        python-dev=2.7.15-r3 \
+        py-pip=10.0.1-r0 \
+        py-curl=7.43.0-r5 \
+        zlib-dev=1.2.11-r1 \
+        make=4.2.1-r2 \
+        ncurses-dev=6.1_p20180818-r1 \
+        g++=6.4.0-r9 \
+        bash=4.4.19-r1 \
+        procps=3.3.15-r0
+
+RUN --mount=type=cache,target=/root/.cache/pip \
+    pip install numpy==1.16.5 && \
+    pip install pandas==0.24.2 tqdm==4.64.1 futures==3.4.0 bgreference==0.6 biopython==1.76 pyliftover==0.4.1
+
+RUN --mount=type=bind,target=/files \
+    mkdir -p /hotmaps && \
+    cp -a /files/hotmaps.sh /files/scripts /hotmaps/ && \
+    chmod -R a+r,a+x /hotmaps/
+
+ENTRYPOINT [ "/bin/sh", "/hotmaps/hotmaps.sh" ]
diff --git a/build/containers/intogen-hotmaps/hotmaps.sh b/build/containers/intogen-hotmaps/hotmaps.sh
new file mode 100755
index 00000000..ae755cd8
--- /dev/null
+++ b/build/containers/intogen-hotmaps/hotmaps.sh
@@ -0,0 +1,144 @@
+#!/bin/bash
+set -x
+
+# Script arguments
+INPUT_FILE=$1
+OUTPUT_FOLDER=$2
+SIGNATURE_FILE=$3
+DATA_FOLDER=$4
+CORES=$5
+
+# Enviroment variables
+HYPERMUT=1000
+SCRIPTS_FOLDER="/hotmaps/scripts"
+
+DATASETS_FOLDER=$INTOGEN_DATASETS/hotmaps
+
+# Functions
+
+exit_on_error() {
+    exit_code=$1
+    if [ "${exit_code}" != "0" ]; then
+        exit "${exit_code}"
+    fi
+}
+
+# Preprocess
+input_name=$(basename "${INPUT_FILE}")
+name=${input_name%.in.maf}
+
+TEMP_FOLDER="$OUTPUT_FOLDER/${name}.tmp"
+mkdir -p "${TEMP_FOLDER}"
+
+input_filename=${name}.maf
+cp "${INPUT_FILE}" "${TEMP_FOLDER}/${input_filename}"
+
+
+# TODO remove the file checks
+
+## STEP1. Map to Structure (output: non_filtered_mupit.INPUT_FILENAME)
+if [ ! -f "${TEMP_FOLDER}/non_filtered_mupit.${input_filename}" ]
+then
+    python $SCRIPTS_FOLDER/map_maf_to_structure.py \
+        --data-dir "${TEMP_FOLDER}" \
+        --match-regex "${input_filename}" \
+        --output-dir "${TEMP_FOLDER}" \
+        --database "${DATA_FOLDER}/mupit_database.db"
+    exit_on_error $?
+fi
+
+## STEP2. Convert MAF to MUPIT (output: coverage_info.txt, INPUT_FILENAME.mupit )
+if [ ! -f "${TEMP_FOLDER}/${input_filename}.mupit" ]
+then
+    python $SCRIPTS_FOLDER/convert_maf_to_mupit.py \
+        --maf "${TEMP_FOLDER}/${input_filename}" \
+        --tumor-type "${name}" \
+        --no-stratify \
+        -mt "${HYPERMUT}" \
+        -i "${TEMP_FOLDER}" \
+        --output "${TEMP_FOLDER}/${input_filename}.mupit" \
+        --database "${DATA_FOLDER}/mupit_database.db"
+    exit_on_error $?
+fi
+
+## STEP3. Filter hypermutated (output: mupit.INPUT_FILENAME)
+if [ ! -f "${TEMP_FOLDER}/mupit.${input_filename}" ]
+then
+    python $SCRIPTS_FOLDER/filter_hypermutated.py \
+        --raw-dir "${TEMP_FOLDER}" \
+        --match-regex "${input_filename}" \
+        --mut-threshold "${HYPERMUT}" \
+        --sample-col 'Tumor_Sample_Barcode' \
+        --data-dir "${TEMP_FOLDER}"
+    exit_on_error $?
+fi
+
+## STEP4. Count mutations (input: mupit.* output: collected.INPUT_FILENAME)
+if [ ! -f "${TEMP_FOLDER}/collected.${input_filename}" ]
+then
+    python "${SCRIPTS_FOLDER}/count_mutations.py" \
+        --data-dir "${TEMP_FOLDER}"
+    exit_on_error $?
+fi
+
+## STEP5. Format mutations table (input: collected.* output: mutation_tcga.INPUT_FILENAME.txt)
+if [ ! -f "${TEMP_FOLDER}/mutation_tcga.${input_filename}" ]
+then
+    python "${SCRIPTS_FOLDER}/format_mutations_table.py" \
+    	--data-dir "${TEMP_FOLDER}"
+    exit_on_error $?
+fi
+
+## STEP7. Run HotMAPS (input: mutation_tcga.NAME.txt output:hotspot_INPUT_FILENAME)
+if [ ! -f "${TEMP_FOLDER}/hotspot_${input_filename}" ]
+then
+    python "${SCRIPTS_FOLDER}/hotspot.py" \
+        --log-level=INFO \
+        -m "${TEMP_FOLDER}/mutation_tcga.${name}.txt" \
+        -a "${DATA_FOLDER}/fully_described_pdb_info.txt" \
+        -t EVERY -n 10000 -r 10.0 -c "${CORES}" \
+        -o "${TEMP_FOLDER}/hotspot_${input_filename}" \
+        -e "${TEMP_FOLDER}/${input_filename}.err --log=stdout" \
+        -gc "${DATASETS_FOLDER}/coordinates.txt.gz" \
+        -S "${SIGNATURE_FILE}" \
+        --maf "${TEMP_FOLDER}/${input_filename}" \
+        --database "${DATA_FOLDER}/mupit_database.db" \
+        --pdb "${DATA_FOLDER}/pdb"
+    exit_on_error $?
+fi
+
+## STEP8. Multiple test
+if [ ! -f "${TEMP_FOLDER}/mtco_${input_filename}" ]
+then
+    python "${SCRIPTS_FOLDER}/multiple_testing_correction.py" \
+        -i "${TEMP_FOLDER}/hotspot_${input_filename}" \
+        -f min -q 0.05 \
+        -m "${TEMP_FOLDER}/${input_filename}.mupit" \
+        -o "${TEMP_FOLDER}/mtco_${input_filename}" \
+        -s "${TEMP_FOLDER}/mtcs_${input_filename}"
+    exit_on_error $?
+fi
+
+## STEP9. Find Hotspots regions gene
+if [ ! -f "${TEMP_FOLDER}/hotspot_gene_${input_filename}" ]
+then
+    python "${SCRIPTS_FOLDER}/find_hotspot_regions_gene.py" \
+        -m "${TEMP_FOLDER}/mtco_${input_filename}" \
+        -a "${TEMP_FOLDER}/${input_filename}.mupit" \
+        -p "${DATA_FOLDER}/fully_described_pdb_info.txt" \
+        -r 10.0 -q 0.05 \
+        -o "${TEMP_FOLDER}/hotspot_gene_${input_filename}" \
+        --pdb "${DATA_FOLDER}/pdb"
+    exit_on_error $?
+fi
+
+## STEP10. Output parser
+if [ ! -f "$OUTPUT_FOLDER/${name}.out.gz" ]
+then
+    python "${SCRIPTS_FOLDER}/postprocess.py" \
+    	"${TEMP_FOLDER}/hotspot_gene_${input_filename}" \
+    	"${TEMP_FOLDER}/mtco_${input_filename}" \
+    	"${OUTPUT_FOLDER}/${name}.out.gz" \
+    	"${OUTPUT_FOLDER}/${name}.clusters.gz"
+    exit_on_error $?
+fi
diff --git a/build/containers/hotmaps/scripts/convert_maf_to_mupit.py b/build/containers/intogen-hotmaps/scripts/convert_maf_to_mupit.py
similarity index 100%
rename from build/containers/hotmaps/scripts/convert_maf_to_mupit.py
rename to build/containers/intogen-hotmaps/scripts/convert_maf_to_mupit.py
diff --git a/build/containers/hotmaps/scripts/count_mutations.py b/build/containers/intogen-hotmaps/scripts/count_mutations.py
similarity index 100%
rename from build/containers/hotmaps/scripts/count_mutations.py
rename to build/containers/intogen-hotmaps/scripts/count_mutations.py
diff --git a/build/containers/hotmaps/scripts/filter_hypermutated.py b/build/containers/intogen-hotmaps/scripts/filter_hypermutated.py
similarity index 100%
rename from build/containers/hotmaps/scripts/filter_hypermutated.py
rename to build/containers/intogen-hotmaps/scripts/filter_hypermutated.py
diff --git a/build/containers/hotmaps/scripts/find_hotspot_regions_gene.py b/build/containers/intogen-hotmaps/scripts/find_hotspot_regions_gene.py
similarity index 100%
rename from build/containers/hotmaps/scripts/find_hotspot_regions_gene.py
rename to build/containers/intogen-hotmaps/scripts/find_hotspot_regions_gene.py
diff --git a/build/containers/hotmaps/scripts/format_mutations_table.py b/build/containers/intogen-hotmaps/scripts/format_mutations_table.py
similarity index 100%
rename from build/containers/hotmaps/scripts/format_mutations_table.py
rename to build/containers/intogen-hotmaps/scripts/format_mutations_table.py
diff --git a/build/containers/hotmaps/scripts/get_hotspot_residues.py b/build/containers/intogen-hotmaps/scripts/get_hotspot_residues.py
similarity index 100%
rename from build/containers/hotmaps/scripts/get_hotspot_residues.py
rename to build/containers/intogen-hotmaps/scripts/get_hotspot_residues.py
diff --git a/build/containers/hotmaps/scripts/hotspot.py b/build/containers/intogen-hotmaps/scripts/hotspot.py
similarity index 100%
rename from build/containers/hotmaps/scripts/hotspot.py
rename to build/containers/intogen-hotmaps/scripts/hotspot.py
diff --git a/build/containers/hotmaps/scripts/maf_utils.py b/build/containers/intogen-hotmaps/scripts/maf_utils.py
similarity index 100%
rename from build/containers/hotmaps/scripts/maf_utils.py
rename to build/containers/intogen-hotmaps/scripts/maf_utils.py
diff --git a/build/containers/hotmaps/scripts/map_maf_to_structure.py b/build/containers/intogen-hotmaps/scripts/map_maf_to_structure.py
similarity index 100%
rename from build/containers/hotmaps/scripts/map_maf_to_structure.py
rename to build/containers/intogen-hotmaps/scripts/map_maf_to_structure.py
diff --git a/build/containers/hotmaps/scripts/multiple_testing_correction.py b/build/containers/intogen-hotmaps/scripts/multiple_testing_correction.py
similarity index 100%
rename from build/containers/hotmaps/scripts/multiple_testing_correction.py
rename to build/containers/intogen-hotmaps/scripts/multiple_testing_correction.py
diff --git a/build/containers/hotmaps/scripts/postprocess.py b/build/containers/intogen-hotmaps/scripts/postprocess.py
similarity index 100%
rename from build/containers/hotmaps/scripts/postprocess.py
rename to build/containers/intogen-hotmaps/scripts/postprocess.py
diff --git a/build/containers/hotmaps/scripts/src/__init__.py b/build/containers/intogen-hotmaps/scripts/src/__init__.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/__init__.py
rename to build/containers/intogen-hotmaps/scripts/src/__init__.py
diff --git a/build/containers/hotmaps/scripts/src/density.py b/build/containers/intogen-hotmaps/scripts/src/density.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/density.py
rename to build/containers/intogen-hotmaps/scripts/src/density.py
diff --git a/build/containers/hotmaps/scripts/src/graph.py b/build/containers/intogen-hotmaps/scripts/src/graph.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/graph.py
rename to build/containers/intogen-hotmaps/scripts/src/graph.py
diff --git a/build/containers/hotmaps/scripts/src/mutations.py b/build/containers/intogen-hotmaps/scripts/src/mutations.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/mutations.py
rename to build/containers/intogen-hotmaps/scripts/src/mutations.py
diff --git a/build/containers/hotmaps/scripts/src/pdb_structure.py b/build/containers/intogen-hotmaps/scripts/src/pdb_structure.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/pdb_structure.py
rename to build/containers/intogen-hotmaps/scripts/src/pdb_structure.py
diff --git a/build/containers/hotmaps/scripts/src/randomizer_aa.py b/build/containers/intogen-hotmaps/scripts/src/randomizer_aa.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/randomizer_aa.py
rename to build/containers/intogen-hotmaps/scripts/src/randomizer_aa.py
diff --git a/build/containers/hotmaps/scripts/src/simulate_mutations_signatures.py b/build/containers/intogen-hotmaps/scripts/src/simulate_mutations_signatures.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/simulate_mutations_signatures.py
rename to build/containers/intogen-hotmaps/scripts/src/simulate_mutations_signatures.py
diff --git a/build/containers/hotmaps/scripts/src/simulation_signatures.py b/build/containers/intogen-hotmaps/scripts/src/simulation_signatures.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/simulation_signatures.py
rename to build/containers/intogen-hotmaps/scripts/src/simulation_signatures.py
diff --git a/build/containers/hotmaps/scripts/src/statistics.py b/build/containers/intogen-hotmaps/scripts/src/statistics.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/statistics.py
rename to build/containers/intogen-hotmaps/scripts/src/statistics.py
diff --git a/build/containers/hotmaps/scripts/src/utils.py b/build/containers/intogen-hotmaps/scripts/src/utils.py
similarity index 100%
rename from build/containers/hotmaps/scripts/src/utils.py
rename to build/containers/intogen-hotmaps/scripts/src/utils.py
diff --git a/build/containers/intogen-mutpanning/Dockerfile b/build/containers/intogen-mutpanning/Dockerfile
new file mode 100644
index 00000000..0d681cbe
--- /dev/null
+++ b/build/containers/intogen-mutpanning/Dockerfile
@@ -0,0 +1,46 @@
+FROM debian:buster-slim AS build
+
+ENV LC_ALL=C.UTF-8
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends --no-install-suggests \
+        openjdk-11-jdk-headless=11.0.23+9-1~deb10u1 \
+        git=1:2.20.1-2+deb10u9 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN git clone https://github.com/genepattern/MutPanning.git --branch v2 && \
+    cd MutPanning && \
+    javac -cp bin/commons-math3-3.6.1.jar:bin/jdistlib-0.4.5-bin.jar \
+          src/AffinityCount_Cosmic.java src/AffinityCount.java src/AlignHG19.java \
+          src/CBASE_Solutions.java src/ClusteringEntity.java src/ClusteringPanCancer.java \
+          src/ComputeMutationRateClusters_Entities.java src/ComputeSignificance.java \
+          src/CountDestructiveMutations.java src/Filter_Step1.java src/Filter_Step2.java \
+          src/Filter_Step3.java src/MutPanning.java src/ReformatCBASE.java -d bin && \
+    cd bin && \
+    printf "Manifest-Version: 1.0\nMain-Class: MutPanning\nClass-Path: commons-math3-3.6.1.jar jdistlib-0.4.5-bin.jar\n" >MANIFEST.MF && \
+    jar cfm MutPanning.jar MANIFEST.MF ./*.class && \
+    rm ./*.class MANIFEST.MF
+
+FROM debian:buster-slim AS final
+
+ENV LC_ALL=C.UTF-8
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends --no-install-suggests \
+        openjdk-11-jre-headless=11.0.23+9-1~deb10u1 \
+        python3.7-minimal=3.7.3-2+deb10u7 \
+        procps=2:3.3.15-2 && \
+    apt-get remove -y python3-pip && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN mkdir -p /mutpanning
+COPY --from=build /MutPanning/bin/*.jar /mutpanning/
+
+# argument 0: root file, where all the other files can be found
+# argument 1: maf file (standard value: root file/MutationsComplete.maf)
+# argument 2: sample annotation file (standard value: root file/SamplesComplete.txt)
+# argument 3: path to Hg19 folder (standard value root file/Hg19/)
+# java -cp MutPanning.jar MutPanning <path_to_outputs> <mutation_file.maf> <samples_file.txt> Hg19/
+ENTRYPOINT [ "/usr/bin/java", "-cp", "/mutpanning/MutPanning.jar", "MutPanning" ]
diff --git a/build/containers/intogen-oncodriveclustl/Dockerfile b/build/containers/intogen-oncodriveclustl/Dockerfile
new file mode 100644
index 00000000..00f94971
--- /dev/null
+++ b/build/containers/intogen-oncodriveclustl/Dockerfile
@@ -0,0 +1,6 @@
+FROM python:3.12-slim
+
+RUN --mount=type=cache,target=/root/.cache/pip \
+    pip3 install oncodriveclustl==1.1.3
+
+ENTRYPOINT [ "/usr/local/bin/oncodriveclustl" ]
diff --git a/build/containers/intogen-oncodrivefml/Dockerfile b/build/containers/intogen-oncodrivefml/Dockerfile
new file mode 100644
index 00000000..97132001
--- /dev/null
+++ b/build/containers/intogen-oncodrivefml/Dockerfile
@@ -0,0 +1,15 @@
+FROM python:3.6-slim
+
+ENV BBGLAB_HOME=/oncodrivefml
+
+RUN --mount=type=cache,target=/root/.cache/pip \
+    pip install oncodrivefml==2.1.3
+
+RUN --mount=type=bind,target=/files \
+    mkdir -p /oncodrivefml && \
+    cp /files/oncodrivefml_v2.conf /oncodrivefml/ && \
+    chmod -R a+r /oncodrivefml
+
+WORKDIR /oncodrivefml
+
+ENTRYPOINT [ "/usr/local/bin/oncodrivefml" ]
diff --git a/build/containers/oncodrivefml/oncodrivefml_v2.conf b/build/containers/intogen-oncodrivefml/oncodrivefml_v2.conf
similarity index 100%
rename from build/containers/oncodrivefml/oncodrivefml_v2.conf
rename to build/containers/intogen-oncodrivefml/oncodrivefml_v2.conf
diff --git a/build/containers/intogen-signature/Dockerfile b/build/containers/intogen-signature/Dockerfile
new file mode 100644
index 00000000..bd3e9756
--- /dev/null
+++ b/build/containers/intogen-signature/Dockerfile
@@ -0,0 +1,4 @@
+FROM python:3.12-slim
+
+RUN --mount=type=cache,target=/root/.cache/pip \
+    pip3 install bgsignature==0.2
diff --git a/build/containers/intogen-smregions/Dockerfile b/build/containers/intogen-smregions/Dockerfile
new file mode 100644
index 00000000..95613390
--- /dev/null
+++ b/build/containers/intogen-smregions/Dockerfile
@@ -0,0 +1,15 @@
+FROM python:3.12-slim
+
+ENV BBGLAB_HOME=/smregions
+
+RUN --mount=type=cache,target=/root/.cache/pip \
+    pip install https://bitbucket.org/bbglab/smregions/get/master.tar.gz
+
+RUN --mount=type=bind,target=/files \
+    mkdir -p /smregions && \
+    cp /files/smregions.conf /smregions && \
+    chmod -R a+r /smregions
+
+WORKDIR /smregions
+
+ENTRYPOINT [ "/usr/local/bin/smregions" ]
diff --git a/build/containers/smregions/smregions.conf b/build/containers/intogen-smregions/smregions.conf
similarity index 100%
rename from build/containers/smregions/smregions.conf
rename to build/containers/intogen-smregions/smregions.conf
diff --git a/build/containers/intogen-transvar/Dockerfile b/build/containers/intogen-transvar/Dockerfile
new file mode 100644
index 00000000..0615b880
--- /dev/null
+++ b/build/containers/intogen-transvar/Dockerfile
@@ -0,0 +1,10 @@
+FROM zhouwanding/transvar:2.5.9
+
+ENV LC_ALL=C.UTF-8
+ENV TRANSVAR_CFG=/data/transvar.cfg
+ENV TRANSVAR_DOWNLOAD_DIR=/data
+
+RUN rm -rf /anno && \
+    mkdir -p /data
+
+ENTRYPOINT [ "/usr/local/bin/transvar" ]
diff --git a/build/containers/mutpanning/Singularity b/build/containers/mutpanning/Singularity
deleted file mode 100644
index 562c6df1..00000000
--- a/build/containers/mutpanning/Singularity
+++ /dev/null
@@ -1,32 +0,0 @@
-Bootstrap: docker
-From: debian:buster-slim
-
-%environment
-    export LC_ALL=C.UTF-8
-
-%runscript
-    exec "/usr/bin/java" "-cp" "/mutpanning/MutPanning.jar" "MutPanning" "$@"
-	# argument 0: root file, where all the other files can be found
-	# argument 1: maf file (standard value: root file/MutationsComplete.maf)
-	# argument 2: sample annotation file (standard value: root file/SamplesComplete.txt)
-	# argument 3: path to Hg19 folder (standard value root file/Hg19/)
-	# java -cp MutPanning.jar MutPanning <path_to_outputs> <mutation_file.maf> <samples_file.txt> Hg19/
-
-%setup
-    mkdir ${SINGULARITY_ROOTFS}/mutpanning
-    cp MutPanning.jar ${SINGULARITY_ROOTFS}/mutpanning/
-    chmod -R a+rx ${SINGULARITY_ROOTFS}/mutpanning/
-
-%post
-    # Load environment
-    export LC_ALL=C.UTF-8
-
-    # Install dependencies
-    apt update
-    # apt upgrade -y
-    apt install -y openjdk-11-jre python3 procps
-
-    # Clean unused things
-    apt-get clean
-    apt remove -y python3-pip
-    rm -rf /var/lib/apt/lists/*
diff --git a/build/containers/mutpanning/mutpanning.mk b/build/containers/mutpanning/mutpanning.mk
deleted file mode 100644
index 9538a61e..00000000
--- a/build/containers/mutpanning/mutpanning.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-
-MUTPANNING_CONTAINER = $(INTOGEN_CONTAINERS)/mutpanning.simg
-
-mutpanning_container_srcdir = ${src_containers}/mutpanning
-
-mutpanning_container_src = ${mutpanning_container_srcdir}/MutPanning.jar \
-	${mutpanning_container_srcdir}/Singularity
-
-
-$(MUTPANNING_CONTAINER): $(mutpanning_container_src) | $(INTOGEN_CONTAINERS)
-	@echo Building MutPanning container
-	${container_builder} ${mutpanning_container_srcdir} $@
-
-CONTAINERS_SUDO += $(MUTPANNING_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/oncodriveclustl/Singularity b/build/containers/oncodriveclustl/Singularity
deleted file mode 100644
index 239ad5d6..00000000
--- a/build/containers/oncodriveclustl/Singularity
+++ /dev/null
@@ -1,6 +0,0 @@
-Bootstrap: docker
-From: python:3
-
-%post
-    # Install OncodriveCLUSTL
-    pip3 --no-cache-dir install oncodriveclustl
\ No newline at end of file
diff --git a/build/containers/oncodriveclustl/clustl.mk b/build/containers/oncodriveclustl/clustl.mk
deleted file mode 100644
index 5812dfeb..00000000
--- a/build/containers/oncodriveclustl/clustl.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-
-CLUSTL_CONTAINER = $(INTOGEN_CONTAINERS)/oncodriveclustl.simg
-
-clustl_container_srcdir = ${src_containers}/oncodriveclustl
-
-clustl_container_src = ${clustl_container_srcdir}/Singularity
-
-$(CLUSTL_CONTAINER): $(clustl_container_src) | $(INTOGEN_CONTAINERS)
-	@echo Building OncodriveCLUSTL container
-	${container_builder} ${clustl_container_srcdir} $@
-
-CONTAINERS_SUDO += $(CLUSTL_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/oncodrivefml/Singularity b/build/containers/oncodrivefml/Singularity
deleted file mode 100644
index 69a3214f..00000000
--- a/build/containers/oncodrivefml/Singularity
+++ /dev/null
@@ -1,17 +0,0 @@
-Bootstrap: docker
-From: python:3.6
-
-%environment
-    export BBGLAB_HOME=/oncodrivefml
-
-%runscript
-
-%setup
-    mkdir ${SINGULARITY_ROOTFS}/oncodrivefml
-    cp oncodrivefml_v2.conf ${SINGULARITY_ROOTFS}/oncodrivefml/
-    chmod -R a+rx ${SINGULARITY_ROOTFS}/oncodrivefml/
-
-%post
-
-    # Install OncodriveFML
-    pip --no-cache-dir install oncodrivefml
diff --git a/build/containers/oncodrivefml/fml.mk b/build/containers/oncodrivefml/fml.mk
deleted file mode 100644
index 2d88359f..00000000
--- a/build/containers/oncodrivefml/fml.mk
+++ /dev/null
@@ -1,13 +0,0 @@
-
-FML_CONTAINER = $(INTOGEN_CONTAINERS)/oncodrivefml.simg
-
-fml_container_srcdir = ${src_containers}/oncodrivefml
-
-fml_container_src = ${fml_container_srcdir}/oncodrivefml_v2.conf \
-	${fml_container_srcdir}/Singularity
-
-$(FML_CONTAINER): $(fml_container_src) | $(INTOGEN_CONTAINERS)
-	@echo Building OncodriveFML container
-	${container_builder} ${fml_container_srcdir} $@
-
-CONTAINERS_SUDO += $(FML_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/signature/Singularity b/build/containers/signature/Singularity
deleted file mode 100644
index 0c8918cf..00000000
--- a/build/containers/signature/Singularity
+++ /dev/null
@@ -1,5 +0,0 @@
-Bootstrap: docker
-From: python:3
-
-%post
-	pip install bgsignature
diff --git a/build/containers/signature/signature.mk b/build/containers/signature/signature.mk
deleted file mode 100644
index f9f11d38..00000000
--- a/build/containers/signature/signature.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-
-SIGNATURE_CONTAINER = $(INTOGEN_CONTAINERS)/signature.simg
-
-signature_container_srcdir = ${src_containers}/signature
-
-signature_container_src = ${signature_container_srcdir}/Singularity
-
-$(SIGNATURE_CONTAINER): ${signature_container_src} | $(INTOGEN_CONTAINERS)
-	@echo Building bgSignature container
-	${container_builder} ${signature_container_srcdir} $@
-
-CONTAINERS_SUDO += $(SIGNATURE_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/smregions/Singularity b/build/containers/smregions/Singularity
deleted file mode 100644
index c1aee28b..00000000
--- a/build/containers/smregions/Singularity
+++ /dev/null
@@ -1,18 +0,0 @@
-Bootstrap: docker
-From: python:3
-
-%environment
-    export BBGLAB_HOME=/smregions
-
-%runscript
-    exec "/usr/local/bin/smregions" "$@"
-
-%setup
-    mkdir ${SINGULARITY_ROOTFS}/smregions
-    cp smregions.conf ${SINGULARITY_ROOTFS}/smregions/
-    chmod -R a+r,a+x ${SINGULARITY_ROOTFS}/smregions/
-
-%post
-
-    # Install SMRegions
-    pip --no-cache-dir install https://bitbucket.org/bbglab/smregions/get/master.tar.gz
diff --git a/build/containers/smregions/smregions.mk b/build/containers/smregions/smregions.mk
deleted file mode 100644
index 6f286c9d..00000000
--- a/build/containers/smregions/smregions.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-
-SMREGIONS_CONTAINER = $(INTOGEN_CONTAINERS)/smregions.simg
-
-smregions_container_srcdir = ${src_containers}/smregions
-
-smregions_container_src = ${smregions_container_srcdir}/smregions.conf \
-	 ${smregions_container_srcdir}/Singularity
-
-$(SMREGIONS_CONTAINER): $(smregions_container_src) | $(INTOGEN_CONTAINERS)
-	@echo Building SMRegions container
-	${container_builder} ${smregions_container_srcdir} $@
-
-
-CONTAINERS_SUDO += $(SMREGIONS_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/transvar/Singularity b/build/containers/transvar/Singularity
deleted file mode 100644
index 9eb8ff02..00000000
--- a/build/containers/transvar/Singularity
+++ /dev/null
@@ -1,18 +0,0 @@
-Bootstrap: docker
-From: zhouwanding/transvar
-
-%environment
-    LC_ALL=C.UTF-8
-    TRANSVAR_CFG=/data/transvar.cfg
-    TRANSVAR_DOWNLOAD_DIR=/data
-    export LC_ALL TRANSVAR_CFG TRANSVAR_DOWNLOAD_DIR
-
-%runscript
-    exec "/usr/local/bin/transvar" "$@"
-
-%post
-	rm -rf /anno
-    mkdir /data
-    
-%test
-    transvar --help
\ No newline at end of file
diff --git a/build/containers/transvar/transvar.mk b/build/containers/transvar/transvar.mk
deleted file mode 100644
index 80b539b8..00000000
--- a/build/containers/transvar/transvar.mk
+++ /dev/null
@@ -1,16 +0,0 @@
-
-#$(CONTAINER_TRANSVAR): | $(INTOGEN_CONTAINERS)
-#	singularity build $@ docker://zhouwanding/transvar
-
-
-TRANSVAR_CONTAINER = $(INTOGEN_CONTAINERS)/transvar.simg
-
-transvar_container_srcdir = ${src_containers}/transvar
-
-transvar_container_src = ${transvar_container_srcdir}/Singularity
-
-$(TRANSVAR_CONTAINER): $(transvar_container_src) | $(INTOGEN_CONTAINERS)
-	@echo Building TransVar container
-	${container_builder} ${transvar_container_srcdir} $@
-
-CONTAINERS_SUDO += $(TRANSVAR_CONTAINER)
\ No newline at end of file
diff --git a/build/containers/vep/releases.txt b/build/containers/vep/releases.txt
deleted file mode 100644
index 42c96f72..00000000
--- a/build/containers/vep/releases.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-111.0
-110.0
-101.0
-100.4
-99.2
-98.3
-97.4
-96.3
-95.3
-94.5
-93.7
-92.1
-91.3
-90.10
-89.9
-88.14
\ No newline at end of file
diff --git a/build/containers/vep/vep.mk b/build/containers/vep/vep.mk
deleted file mode 100644
index 26f684fb..00000000
--- a/build/containers/vep/vep.mk
+++ /dev/null
@@ -1,13 +0,0 @@
-
-# Docs on the VEP docker image: https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#docker
-
-VEP_CONTAINER = $(INTOGEN_CONTAINERS)/vep.simg
-
-vep_container_releases_file = ${src_containers}/vep/releases.txt
-vep_container_version = `grep "^${ensembl}" ${vep_container_releases_file}`
-
-$(VEP_CONTAINER): $(vep_container_releases_file) $$(ENSEMBL) | $(INTOGEN_CONTAINERS)
-	@echo Building VEP container
-	singularity build $@ docker://ensemblorg/ensembl-vep:release_${vep_container_version}
-
-CONTAINERS_USER += $(VEP_CONTAINER)
diff --git a/combination/Dockerfile b/combination/Dockerfile
new file mode 100644
index 00000000..dedeb56c
--- /dev/null
+++ b/combination/Dockerfile
@@ -0,0 +1,17 @@
+FROM python:3.9-slim
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends --no-install-suggests build-essential=12.9 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN --mount=type=cache,target=/root/.cache/pip \
+    --mount=type=bind,target=/files \
+    mkdir -p /combination && \
+    cd /files && \
+    cp -a intogen_combination /combination/ && \
+    cp LICENSE.txt MANIFEST.in README.rst requirements.txt setup.py /combination/ && \
+    pip install /combination
+
+ENTRYPOINT [ "/usr/local/bin/intogen-combine" ]
diff --git a/core/Dockerfile b/core/Dockerfile
new file mode 100644
index 00000000..ae25c3b4
--- /dev/null
+++ b/core/Dockerfile
@@ -0,0 +1,21 @@
+FROM python:3.12-slim
+
+ENV LC_ALL=C.UTF-8
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends --no-install-suggests \
+        build-essential=12.9 \
+        zlib1g-dev=1:1.2.13.dfsg-1 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN --mount=type=cache,target=/root/.cache/pip \
+    --mount=type=bind,target=/files \
+    pip install open-variant==1.0.0 && \
+    mkdir -p /core && \
+    cd /files && \
+    cp -a intogen_core /combination/ && \
+    cp LICENSE.txt MANIFEST.in README.rst requirements.txt setup.py /core/ && \
+    pip install /core && \
+    cp /files/get_field.sh /usr/local/bin/ && \
+    chmod a+rx /usr/local/bin/get_field.sh
diff --git a/core/get_field.sh b/core/get_field.sh
new file mode 100755
index 00000000..2dfb0423
--- /dev/null
+++ b/core/get_field.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+input=$1
+field=$2
+
+C=1
+header=$( zcat "${input}" | head -n 1 )
+for i in ${header}
+do
+	if [[ "$i" == "${field}" ]]
+	then
+		break
+	else
+		C=$(( C + 1 ))
+	fi
+done
+
+zcat "${input}" | sed -n '2p' | cut -f$C | xargs printf