diff --git a/.github/workflows/docker_build_publish_develop.yml b/.github/workflows/docker_build_publish_develop.yml
index fde5a4faf..6a9a55f0a 100644
--- a/.github/workflows/docker_build_publish_develop.yml
+++ b/.github/workflows/docker_build_publish_develop.yml
@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, ascatNgs, cadd, cnvkit, cnvpytor, coverage_qc, delly, gatk, htslib, multiqc, msisensorpro, purecn, somalier, varcall_py3, varcall_py27, vcf2cytosure]
+        container-name: [varcall_py3]
     steps:
       - name: Git checkout
         id: git_checkout
diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 141861c72..b1d0cda53 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -1,22 +1,46 @@
 FROM continuumio/miniconda3:4.10.3-alpine
 
-LABEL base.image="continuumio/miniconda3:4.10.3-alpine"
-LABEL about.home="https://github.com/Clinical-Genomics/BALSAMIC"
-LABEL about.documentation="https://balsamic.readthedocs.io/"
-LABEL about.license="MIT License (MIT)"
-LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
+LABEL base.image="continuumio/miniconda3:4.10.3-alpine" \
+      about.home="https://github.com/Clinical-Genomics/BALSAMIC" \
+      about.documentation="https://balsamic.readthedocs.io/" \
+      about.license="MIT License (MIT)" \
+      about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
 
 ENV PATH="/opt/conda/bin/:${PATH}"
 
-RUN apk add --no-cache bash gcc git
+# Install necessary packages
+RUN apk add --no-cache bash gcc git musl-dev
 
-ARG WORK_DIR=project
 ARG CONTAINER_NAME
 
-# Copy all project files
-COPY . /${WORK_DIR}
+# Copy the container folder into the image
+COPY BALSAMIC/containers/${CONTAINER_NAME}/ /project/BALSAMIC/containers/${CONTAINER_NAME}/
 
-RUN cd /${WORK_DIR}/BALSAMIC/containers/${CONTAINER_NAME}/ && /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
+# Set the working directory to the container directory
+WORKDIR /project/BALSAMIC/containers/${CONTAINER_NAME}
 
-# Clean work environment
-RUN rm -rf /${WORK_DIR:?} && conda clean --all --yes
+# Run the package installation script
+RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
+
+# Install TIDDIT
+WORKDIR /project
+RUN python -m pip install --no-cache-dir --upgrade cython joblib pip requests && \
+    git clone --depth 1 --branch TIDDIT-3.8.0 https://github.com/SciLifeLab/TIDDIT.git && \
+    cd TIDDIT && \
+    pip install .
+
+# Install fermi2
+WORKDIR /project
+RUN git clone https://github.com/lh3/fermi2.git && \
+    cd fermi2 && \
+    make
+
+# Install bwa (includes ropebwt2)
+WORKDIR /project
+RUN git clone https://github.com/lh3/bwa.git && \
+    cd bwa && \
+    make
+
+# Clean up work environment
+WORKDIR /
+RUN rm -rf /project && conda clean --all --yes
diff --git a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
index 4f106103e..d7089f19b 100644
--- a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
+++ b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
@@ -1,6 +1,6 @@
 channels:
-  - conda-forge
   - anaconda
+  - conda-forge
   - bioconda
   - defaults
 
@@ -8,30 +8,30 @@ dependencies:
   - _libgcc_mutex=0.1
   - _openmp_mutex=4.5
   - _r-mutex=1.0.1
+  - _sysroot_linux-64_curr_repodata_hack=3
   - bcftools=1.15.1
-  - bfc=r181
   - binutils_impl_linux-64=2.35.1
   - binutils_linux-64=2.35
+  - boltons=24.0.0
   - brotlipy=0.7.0
   - bwa=0.7.17
   - bwidget=1.9.14
   - bzip2=1.0.8
-  - c-ares=1.18.1
-  - ca-certificates=2022.12.7
+  - c-ares=1.32.3
+  - ca-certificates=2024.7.4
   - cairo=1.16.0
-  - certifi=2022.12.7
+  - certifi=2024.7.4
   - cffi=1.14.6
   - chardet=4.0.0
   - click=8.0.4
   - coloredlogs=15.0.1
-  - conda=23.1.0
-  - conda-package-handling=2.0.2
-  - conda-package-streaming=0.7.0
+  - conda=23.7.1
+  - conda-package-handling=2.3.0
+  - conda-package-streaming=0.10.0
   - cryptography=39.0.0
   - curl=7.86.0
   - cyvcf2=0.30.16
-  - expat=2.5.0
-  - fermi2=r193
+  - expat=2.6.2
   - font-ttf-dejavu-sans-mono=2.37
   - font-ttf-inconsolata=3.000
   - font-ttf-source-code-pro=2.038
@@ -41,9 +41,11 @@ dependencies:
   - fonts-conda-forge=1
   - freetype=2.12.1
   - fribidi=1.0.10
+  - gatk=3.8
   - gcc_impl_linux-64=9.3.0
   - gcc_linux-64=9.3.0
-  - gettext=0.21.1
+  - gettext=0.22.5
+  - gettext-tools=0.22.5
   - gfortran_impl_linux-64=9.3.0
   - gfortran_linux-64=9.3.0
   - graphite2=1.3.13
@@ -55,54 +57,61 @@ dependencies:
   - humanfriendly=10.0
   - icu=68.2
   - idna=2.10
-  - joblib=1.2.0
   - jpeg=9e
-  - kernel-headers_linux-64=2.6.32
+  - jsonpatch=1.33
+  - jsonpointer=3.0.0
+  - kernel-headers_linux-64=3.10.0
   - keyutils=1.6.1
   - krb5=1.19.3
   - ld_impl_linux-64=2.35.1
-  - lerc=3.0
+  - lerc=4.0.0
+  - libasprintf=0.22.5
+  - libasprintf-devel=0.22.5
   - libblas=3.9.0
   - libcblas=3.9.0
   - libcurl=7.86.0
-  - libdeflate=1.10
+  - libdeflate=1.13
   - libedit=3.1.20191231
   - libev=4.33
+  - libexpat=2.6.2
   - libffi=3.3
   - libgcc-devel_linux-64=9.3.0
-  - libgcc-ng=12.2.0
+  - libgcc-ng=14.1.0
+  - libgettextpo=0.22.5
+  - libgettextpo-devel=0.22.5
   - libgfortran-ng=9.5.0
   - libgfortran5=9.5.0
   - libglib=2.68.4
-  - libgomp=12.2.0
+  - libgomp=14.1.0
   - libiconv=1.17
   - liblapack=3.9.0
   - libnghttp2=1.51.0
   - libopenblas=0.3.18
-  - libpng=1.6.39
+  - libpng=1.6.43
   - libssh2=1.10.0
   - libstdcxx-devel_linux-64=9.3.0
-  - libstdcxx-ng=12.2.0
+  - libstdcxx-ng=14.1.0
   - libtiff=4.4.0
-  - libuuid=2.32.1
-  - libwebp-base=1.2.4
-  - libxcb=1.13
+  - libuuid=2.38.1
+  - libwebp-base=1.4.0
+  - libxcb=1.16
   - libxml2=2.9.12
   - libzlib=1.2.13
   - make=4.3
-  - ncurses=6.3
-  - numpy=1.24.2
-  - openjdk=8.0.332
-  - openssl=1.1.1t
+  - ncurses=6.5
+  - numpy=1.24.4
+  - openjdk=8.0.412
+  - openssl=1.1.1w
+  - packaging=24.1
   - pango=1.48.10
   - pcre=8.45
   - pcre2=10.37
   - perl=5.26.2
-  - pip=23.0.1
-  - pixman=0.40.0
-  - pluggy=1.0.0
+  - pip=24.2
+  - pixman=0.43.2
+  - pluggy=1.5.0
   - pthread-stubs=0.4
-  - pycosat=0.6.4
+  - pycosat=0.6.6
   - pycparser=2.20
   - pyopenssl=20.0.1
   - pysam=0.19.1
@@ -112,61 +121,57 @@ dependencies:
   - r-base=4.1.1
   - r-bitops=1.0_7
   - r-catools=1.18.2
-  - r-cli=3.6.0
+  - r-cli=3.6.1
   - r-colorspace=2.1_0
   - r-crayon=1.5.2
   - r-ellipsis=0.3.2
   - r-fansi=1.0.4
   - r-farver=2.1.1
-  - r-ggplot2=3.4.1
+  - r-ggplot2=3.4.2
   - r-glue=1.6.2
   - r-gplots=3.1.3
   - r-gsalib=2.2.1
-  - r-gtable=0.3.1
+  - r-gtable=0.3.3
   - r-gtools=3.9.4
   - r-isoband=0.2.7
   - r-kernsmooth=2.23_20
   - r-labeling=0.4.2
-  - r-lattice=0.20_45
+  - r-lattice=0.21_8
   - r-lifecycle=1.0.3
   - r-magrittr=2.0.3
-  - r-mass=7.3_58.2
-  - r-matrix=1.5_3
-  - r-mgcv=1.8_41
+  - r-mass=7.3_58.3
+  - r-matrix=1.5_4.1
+  - r-mgcv=1.8_42
   - r-munsell=0.5.0
   - r-nlme=3.1_155
-  - r-pillar=1.8.1
+  - r-pillar=1.9.0
   - r-pkgconfig=2.0.3
   - r-plyr=1.8.8
   - r-r6=2.5.1
   - r-rcolorbrewer=1.1_3
   - r-rcpp=1.0.10
   - r-reshape=0.8.9
-  - r-rlang=1.0.6
+  - r-rlang=1.1.1
   - r-scales=1.2.1
-  - r-tibble=3.1.8
+  - r-tibble=3.2.1
   - r-utf8=1.2.3
-  - r-vctrs=0.5.2
+  - r-vctrs=0.6.2
   - r-viridislite=0.4.1
   - r-withr=2.5.0
-  - readline=8.1.2
-  - requests=2.25.1
-  - ropebwt2=r187
-  - ruamel.yaml=0.17.21
-  - ruamel.yaml.clib=0.2.7
+  - readline=8.1
+  - ruamel.yaml=0.17.40
+  - ruamel.yaml.clib=0.2.8
   - samtools=1.15.1
   - sed=4.8
-  - seqtk=1.3
-  - setuptools=67.4.0
+  - setuptools=72.1.0
   - six=1.16.0
   - sqlite=3.36.0
   - svdb=2.8.1
-  - sysroot_linux-64=2.12
+  - sysroot_linux-64=2.17
   - tabix=1.11
-  - tiddit=3.3.2
-  - tk=8.6.12
+  - tk=8.6.13
   - tktable=2.10
-  - toolz=0.12.0
+  - toolz=0.12.1
   - tqdm=4.61.2
   - tzdata=2021a
   - urllib3=1.26.6
@@ -175,19 +180,22 @@ dependencies:
   - vcfpy=0.13.4
   - wheel=0.36.2
   - xorg-kbproto=1.0.7
-  - xorg-libice=1.0.10
-  - xorg-libsm=1.2.3
-  - xorg-libx11=1.7.2
-  - xorg-libxau=1.0.9
+  - xorg-libice=1.1.1
+  - xorg-libsm=1.2.4
+  - xorg-libx11=1.8.9
+  - xorg-libxau=1.0.11
   - xorg-libxdmcp=1.1.3
   - xorg-libxext=1.3.4
-  - xorg-libxrender=0.9.10
-  - xorg-libxt=1.2.1
+  - xorg-libxrender=0.9.11
+  - xorg-libxt=1.3.0
   - xorg-renderproto=0.11.1
   - xorg-xextproto=7.3.0
   - xorg-xproto=7.0.31
   - xz=5.2.5
   - yaml=0.2.5
   - zlib=1.2.13
-  - zstandard=0.19.0
-  - zstd=1.5.2
+  - zstandard=0.23.0
+  - zstd=1.5.6
+  - pip:
+      - charset-normalizer==3.3.2
+      - requests==2.32.3
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index b05912b31..e66a08736 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -13,6 +13,7 @@ Changed:
 * `SLEEP_BEFORE_START` to 600s https://github.com/Clinical-Genomics/BALSAMIC/pull/1372
 * Updated Multiqc to version 1.22.3 https://github.com/Clinical-Genomics/BALSAMIC/pull/1441
 * Upgrade `vcf2cytosure` version to 0.9.1 and remove hardcoded versions https://github.com/Clinical-Genomics/BALSAMIC/pull/1456
+* Upgrade `TIDDIT` version to 3.8.0 https://github.com/Clinical-Genomics/BALSAMIC/pull/1470
 
 Removed:
 ^^^^^^^^
diff --git a/docs/balsamic_methods.rst b/docs/balsamic_methods.rst
index 783e2f1c5..c8a37f990 100644
--- a/docs/balsamic_methods.rst
+++ b/docs/balsamic_methods.rst
@@ -36,7 +36,7 @@ The final BAM is quality controlled using WgsMetricsAlgo and CoverageMetrics fro
 Results of the quality controlled steps were summarized by MultiQC v1.12 :superscript:`7`.
 Small somatic mutations (SNVs and INDELs) were called for each sample using Sentieon TNscope :superscript:`16`.
 The called-variants were also further second filtered using the criteria (DP(tumor,normal) >= 10; AD(tumor) >= 3; AF(tumor) >= 0.05, Maximum AF(tumor < 1;  GNOMADAF_popmax <= 0.001; normalized base quality scores >= 20, read_counts of alt,ref alle > 0).
-Structural variants were called using Manta v1.6.0 :superscript:`9`, Delly v1.0.3 :superscript:`10` and TIDDIT v3.3.2 :superscript:`12`.
+Structural variants were called using Manta v1.6.0 :superscript:`9`, Delly v1.0.3 :superscript:`10` and TIDDIT v3.8.0 :superscript:`12`.
 Copy number variations (CNV) were called using ascatNgs v4.5.0 :superscript:`17` (tumor-normal), Delly v1.0.3 :superscript:`10` and CNVpytor v1.3.1 :superscript:`22` (tumor-only) and converted from CNV to deletions (DEL) and duplications (DUP).
 The structural variant (SV) calls from Manta, Delly, TIDDIT, ascatNgs (tumor-normal) and CNVpytor (tumor-only) were merged using SVDB v2.8.1 :superscript:`12`
 The clinical set of SNV and SV is also annotated and filtered against loqusDB curated frequency of observed variants (frequency < 0.01) from non-cancer cases and only annotated using frequency of observed variants from cancer cases (somatic and germline).
diff --git a/docs/bioinfo_softwares.rst b/docs/bioinfo_softwares.rst
index c49b34844..3e752021a 100644
--- a/docs/bioinfo_softwares.rst
+++ b/docs/bioinfo_softwares.rst
@@ -146,7 +146,7 @@ tiddit
 ~~~~~~
 :Source code: `Github` `<https://github.com/SciLifeLab/TIDDIT>`_
 :Article: `F1000Res` `<https://pubmed.ncbi.nlm.nih.gov/28781756/>`_
-:Version: `3.3.2`
+:Version: `3.8.0`
 
 vardict
 ~~~~~~~
diff --git a/tests/test_data/config.json b/tests/test_data/config.json
index ec9a4f511..889577f85 100644
--- a/tests/test_data/config.json
+++ b/tests/test_data/config.json
@@ -205,7 +205,7 @@
     "gatk": ["3.8"],
     "samtools": ["1.15.1", "1.9"],
     "svdb": ["2.8.1"],
-    "tiddit": ["3.3.2"],
+    "tiddit": ["3.8.0"],
     "vardict": ["2019.06.04"],
     "somalier": ["0.2.16"],
     "delly": ["1.0.3"],
diff --git a/tests/test_data/config_pon.json b/tests/test_data/config_pon.json
index 7ef3dd26b..cbff98963 100644
--- a/tests/test_data/config_pon.json
+++ b/tests/test_data/config_pon.json
@@ -70,7 +70,7 @@
     "bwa": ["0.7.17"],
     "gatk": ["3.8"],
     "svdb": ["2.8.1"],
-    "tiddit": ["3.3.2"],
+    "tiddit": ["3.8.0"],
     "vardict": ["2019.06.04"],
     "csvkit": ["1.0.7"],
     "fastp": ["0.23.2"],