diff --git a/README.md b/README.md
index 9796483a086c62c14ac3270ffd7a068fa96cecc0..fec96e2466dd17b76f2adaaf94f53f4ec012d9a0 100755
--- a/README.md
+++ b/README.md
@@ -68,6 +68,7 @@ NextFlow pipeline used by the Developmental Cognitive Neuroscience Lab (DCNL) to
     mkdir images
     apptainer build \
       --mksquashfs-args="-comp lz4" \
+      --build-arg-file="containers/versions.txt" \
       images/debian-nanopore.sif \
       containers/debian-nanopore.def
     ```
diff --git a/containers/debian-nanopore.def b/containers/debian-nanopore.def
index e55c1c18f56def3a5593a502f857596726eb8496..d8d4fa482ce7f29783655c33b443d0cd6ecfbe15 100644
--- a/containers/debian-nanopore.def
+++ b/containers/debian-nanopore.def
@@ -8,12 +8,12 @@ From: debian:12
     locales \
     wget \
     git \
-    jq \
-    python3 \
+    jq="{{ JQ_VERSION }}" \
+    python3="{{ PYTHON3_VERSION }}" \
     python3-pip \
     cython3 \
-    samtools \
-    bedtools \
+    samtools="{{ SAMTOOLS_VERSION }}" \
+    bedtools="{{ BEDTOOLS_VERSION }}" \
     && apt-get clean && rm -rf /var/lib/apt/lists/*
 
     # Set timezone and language for container ##
@@ -27,32 +27,35 @@ From: debian:12
     # using no-cache-dir so we dont keep a copy of the downloaded package
     # and break-system-packages to override PEP 668 (which blocks pip installs)
     pip install --no-cache-dir --break-system-packages \
-    pod5==0.3.23 \
-    multiqc==1.28 \
-    plotly==5.18.0
+    pod5=={{ POD5_VERSION }} \
+    multiqc=={{ MULTIQC_VERSION }} \
+    plotly=={{ PLOTLY_VERSION }}
 
-    # Clone and install pycoQC 3.0.0 from duceppemo fork (altering plotly version to match MultiQC plotly version >= 5.18)
+    # Clone and install pycoQC from duceppemo fork
+    # (change plotly version to match MultiQC plotly version >= 5.18)
     cd /opt
-    git clone https://github.com/duceppemo/pycoQC.git
+    # clone from the CIACD fork
+    git clone https://gmapsrv.pucrs.br/gitlab/ccd-public/pycoQC.git
     cd pycoQC
-    sed -i 's/plotly==5.16.1/plotly==5.18.0/' setup.py
     python3 setup.py install
 
     # Install modkit
     cd /opt
     mkdir modkit && cd modkit
-    wget https://github.com/nanoporetech/modkit/releases/download/v0.4.4/modkit_v0.4.4_u16_x86_64.tar.gz
-    tar -xzf modkit_v0.4.4_u16_x86_64.tar.gz
-    rm modkit_v0.4.4_u16_x86_64.tar.gz
-    echo 'export PATH="/opt/modkit/dist_modkit_v0.4.4_7cf558c:$PATH"' >> "$SINGULARITY_ENVIRONMENT"
+    wget "https://github.com/nanoporetech/modkit/releases/download/{{ MODKIT_VERSION }}/modkit_{{ MODKIT_VERSION }}_u16_x86_64.tar.gz"
+    tar -xzf "modkit_{{ MODKIT_VERSION }}_u16_x86_64.tar.gz"
+    rm "modkit_{{ MODKIT_VERSION }}_u16_x86_64.tar.gz"
+    cd "dist_modkit_{{ MODKIT_VERSION }}"*
+    echo 'export PATH="'"$(pwd)"'/:$PATH"' >> "$SINGULARITY_ENVIRONMENT"
 
     # Install Dorado
     cd /opt
     mkdir dorado && cd dorado
-    wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-1.0.1-linux-x64.tar.gz
-    tar -xzf dorado-1.0.1-linux-x64.tar.gz
-    rm dorado-1.0.1-linux-x64.tar.gz
-    echo 'export PATH="/opt/dorado/dorado-1.0.1-linux-x64/bin/:$PATH"' >> "$SINGULARITY_ENVIRONMENT"
+    wget "https://cdn.oxfordnanoportal.com/software/analysis/dorado-{{ DORADO_VERSION }}-linux-x64.tar.gz"
+    tar -xzf "dorado-{{ DORADO_VERSION }}-linux-x64.tar.gz"
+    rm "dorado-{{ DORADO_VERSION }}-linux-x64.tar.gz"
+    cd "dorado-{{ DORADO_VERSION }}"*
+    echo 'export PATH="'"$(pwd)"'/bin/:$PATH"' >> "$SINGULARITY_ENVIRONMENT"
 
 %test
     # Check if installations are on path and display their versions
@@ -64,22 +67,23 @@ From: debian:12
     samtools --version
     bedtools --version
     jq --version
+    python3 --version
 
 %labels
     author Joao Henrique Chrusciel
-    version v0.5.0
+    version {{ DEBIAN_NANOPORE_VERSION }}
 
 %help
     Software included in the container are:
 
-    dorado==1.0.1
-    modkit==0.4.4
-    samtools==1.16.1
-    pod5==0.3.23
-    pycoQC==2.5.2
-    bedtools==2.30.0
-    multiqc==1.28
-    jq==1.6
+    dorado=={{ DORADO_VERSION }}
+    modkit=={{ MODKIT_VERSION }}
+    samtools=={{ SAMTOOLS_VERSION }}
+    pod5=={{ POD5_VERSION }}
+    pycoQC=={{ PYCOQC_VERION }}
+    bedtools=={{ BEDTOOLS_VERSION }}
+    multiqc=={{ MULTIQC_VERSION }}
+    jq=={{ JQ_VERSION }}
 
     NOTE THAT VERSIONS OF THE SOFTWARE INSTALLED WILL CHANGE THROUGH
     TIME IF YOU BUILD THE IMAGE FROM THE RECIPE FILE.
diff --git a/containers/versions.txt b/containers/versions.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f62054504b70b10936566ce611ae3e0015a2ffe7
--- /dev/null
+++ b/containers/versions.txt
@@ -0,0 +1,11 @@
+DEBIAN_NANOPORE_VERSION="v0.5.2"
+JQ_VERSION="1.6-2.1"
+SAMTOOLS_VERSION="1.16.1-1"
+BEDTOOLS_VERSION="2.30.0+dfsg-3"
+PYTHON3_VERSION="3.11.2-1+b1"
+POD5_VERSION="0.3.23"
+MULTIQC_VERSION="1.28"
+PLOTLY_VERSION="5.18.0"
+PYCOQC_VERION="3.0.0"
+MODKIT_VERSION="v0.4.3"
+DORADO_VERSION="0.9.1"