chore: Bump TIDDIT version

BALSAMIC/containers/varcall_py3/Dockerfile

@@ -1,22 +1,28 @@
 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}"
 
+# Install necessary packages
 RUN apk add --no-cache bash gcc git
 
-ARG WORK_DIR=project
 ARG CONTAINER_NAME
 
-# Copy all project files
-COPY . /${WORK_DIR}
+# Set the working directory
+WORKDIR /project
 
-RUN cd /${WORK_DIR}/BALSAMIC/containers/${CONTAINER_NAME}/ && /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
+# Copy all project files to WORKDIR
+COPY . .
 
-# Clean work environment
-RUN rm -rf /${WORK_DIR:?} && conda clean --all --yes
+# Execute the container specific script
+WORKDIR /project/BALSAMIC/containers/${CONTAINER_NAME}
+RUN /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
+
+# Clean up work environment
+WORKDIR /
+RUN rm -rf /project && conda clean --all --yes

BALSAMIC/containers/varcall_py3/varcall_py3.yaml

@@ -163,7 +163,7 @@ dependencies:
   - svdb=2.8.1
   - sysroot_linux-64=2.12
   - tabix=1.11
-  - tiddit=3.3.2
+  - tiddit=3.8.0
   - tk=8.6.12
   - tktable=2.10
   - toolz=0.12.0

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:
 ^^^^^^^^

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).

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
 ~~~~~~~

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"],

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"],