diff --git a/modules/viquas/Dockerfile b/modules/viquas/Dockerfile
index f35ead5..78a153b 100644
--- a/modules/viquas/Dockerfile
+++ b/modules/viquas/Dockerfile
@@ -6,18 +6,18 @@ ENV R_HOME=/usr/local/lib/R
 ENV TZ=Etc/UTC
 ENV SAMTOOLS_VERSION=1.2
 
-# Install R basic dependencies
-RUN apt-get update && \
+RUN <<END_RUN_CMD
+    # Install R
+    apt-get update
     apt-get install --no-install-recommends -y \
-        sed \
         curl \
         ca-certificates
-RUN curl -L "https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${ROCKER_VERSION}.tar.gz" | tar xvz
-RUN ./rocker-versioned2-R${ROCKER_VERSION}/scripts/install_R.sh
-RUN rm -rf rocker-versioned2-R${ROCKER_VERSION}
+    curl -L "https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${ROCKER_VERSION}.tar.gz" | tar xvz
+    ./rocker-versioned2-R${ROCKER_VERSION}/scripts/install_R.sh
+    rm -rf rocker-versioned2-R${ROCKER_VERSION}
 
-# Install BioPerl
-RUN apt-get update && \
+    # Install BioPerl
+    apt-get update
     apt-get install --no-install-recommends -y \
         curl \
         perl \
@@ -26,33 +26,91 @@ RUN apt-get update && \
         make \
         libexpat1-dev \
         libssl-dev \
-        zlib1g-dev
-RUN cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs
+        zlib1g-dev \
+        libncurses5-dev
+    cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs
 
-# Install R packages
-RUN install2.r --error --skipinstalled BiocManager
-RUN R -e "BiocManager::install(c('Biostrings', 'seqinr'))"
+    # Install R packages
+    install2.r --error --skipinstalled BiocManager
+    R -e "BiocManager::install(c('Biostrings', 'seqinr'))"
 
-# Install samtools
-RUN apt-get update && \
-    apt-get install --no-install-recommends -y libncurses5-dev
-RUN curl -L "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" | tar xvj
-RUN cd samtools-${SAMTOOLS_VERSION} && make && make install && cd ..
-RUN rm -rf samtools-${SAMTOOLS_VERSION}
+    # Install samtools
+    curl -L "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" | tar xvj
+    cd samtools-${SAMTOOLS_VERSION} && make &&  make install && cd ..
+    rm -rf samtools-${SAMTOOLS_VERSION}
 
-# Cleanup
-RUN apt-get remove -y \
-    build-essential \
-    make
+    # Install viquas
+    mkdir /viquas && \
+    curl -L "https://master.dl.sourceforge.net/project/viquas/ViQuaS1.3.tar.gz" | tar xvz -C /viquas --strip-components=1
 
-# Install Viquas
-RUN apt-get update && apt-get install --no-install-recommends -y curl
-RUN mkdir /viquas && curl -L "https://master.dl.sourceforge.net/project/viquas/ViQuaS1.3.tar.gz" | tar xvz -C /viquas --strip-components=1
-RUN apt-get remove -y curl
+    # Cleanup
+    apt-get remove -y \
+        build-essential \
+        make \
+        curl
+    rm -rf /var/lib/apt/lists
+END_RUN_CMD
 
-# Add wrapper script
-COPY viquas /usr/bin/viquas
-RUN chmod +x /usr/bin/viquas
-RUN mkdir /work
+RUN <<END_RUN_CMD
+cat << 'EOF' > /usr/bin/viquas
+#!/bin/sh
+USAGE="
+  USAGE:
+    viquas reference.fsa reads.bam [o r perform_richness diversity_region_length]
+"
+
+NUM_ARGS=$#
+case $NUM_ARGS in
+  2)
+  ;;
+  6)
+  ;;
+  *)
+  echo "${USAGE}"
+  echo "Incorrect number of arguments: expecting 2 or 6"
+  exit 1
+esac
+
+PWD_BACKUP=$PWD
+
+if [ ! -f "${1}" ]; then
+  echo "Error: ${1} is not a file"
+  exit 1
+fi
+
+if [ ! -f "${2}" ]; then
+  echo "Error: ${2} is not a file"
+  exit 1
+fi
+
+REFERENCE_FILE=$(basename "${1}")
+BAM_FILE=$(basename "${2}")
+
+cp "${1}" /viquas
+cp "${2}" /viquas
+
+cd /viquas || exit 1
+
+case $NUM_ARGS in
+  2)
+    Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}"
+  ;;
+  6)
+    Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}" "${@[3:]}"
+  ;;
+  *)
+  echo "${USAGE}"
+  echo "Incorrect number of arguments: expecting 2 or 6"
+  exit 1
+esac
+
+mv /viquas/ViQuaS-Spectrum.fa "${PWD_BACKUP}"
+mv /viquas/ViQuaS-Richness.txt "${PWD_BACKUP}" 2> /dev/null
+
+cd "${PWD_BACKUP}" || exit 1
+EOF
+chmod +x /usr/bin/viquas
+mkdir /work
+END_RUN_CMD
 
 ENTRYPOINT [ "viquas" ]
diff --git a/modules/viquas/viquas b/modules/viquas/viquas
deleted file mode 100755
index 410d59d..0000000
--- a/modules/viquas/viquas
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/bin/sh
-USAGE="
-  USAGE:
-    viquas reference.fsa reads.bam [o r perform_richness diversity_region_length]
-"
-
-NUM_ARGS=$#
-case $NUM_ARGS in
-  2)
-  ;;
-  6)
-  ;;
-  *)
-  echo "${USAGE}"
-  echo "Incorrect number of arguments: expecting 2 or 6"
-  exit 1
-esac
-
-PWD_BACKUP=$PWD
-
-if [ ! -f "${1}" ]; then
-  echo "Error: ${1} is not a file"
-  exit 1
-fi
-
-if [ ! -f "${2}" ]; then
-  echo "Error: ${2} is not a file"
-  exit 1
-fi
-
-REFERENCE_FILE=$(basename "${1}")
-BAM_FILE=$(basename "${2}")
-
-cp "${1}" /viquas
-cp "${2}" /viquas
-
-cd /viquas || exit 1
-
-case $NUM_ARGS in
-  2)
-    Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}"
-  ;;
-  6)
-    Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}" "${@[3:]}"
-  ;;
-  *)
-  echo "${USAGE}"
-  echo "Incorrect number of arguments: expecting 2 or 6"
-  exit 1
-esac
-
-mv /viquas/ViQuaS-Spectrum.fa "${PWD_BACKUP}"
-mv /viquas/ViQuaS-Richness.txt "${PWD_BACKUP}" 2> /dev/null
-
-cd "${PWD_BACKUP}" || exit 1