fix: CNVkit container (#1457)

BALSAMIC/containers/cnvkit/Dockerfile

@@ -1,34 +1,32 @@
 FROM python:3.10-slim
 
-LABEL base.image="python:3.10-slim"
-LABEL maintainer="Clinical Genomics"
-LABEL about.contact="support@clinicalgenomics.se"
-LABEL software="cnvkit"
-LABEL software.version="0.9.10"
-LABEL about.summary="Copy number variant detection from targeted DNA sequencing"
-LABEL about.home="https://github.com/etal/cnvkit"
-LABEL about.documentation="https://cnvkit.readthedocs.io"
-LABEL about.license="MIT License (MIT)"
+LABEL base.image="python:3.10-slim" \
+    maintainer="Clinical Genomics" \
+    about.contact="support@clinicalgenomics.se" \
+    software="CNVkit" \
+    software.version="0.9.10" \
+    about.summary="Copy number variant detection from targeted DNA sequencing" \
+    about.home="https://github.com/etal/cnvkit" \
+    about.documentation="https://cnvkit.readthedocs.io" \
+    about.license="MIT License (MIT)"
 
 ENV DEBIAN_FRONTEND noninteractive
+ENV VENV /opt/venv
+ENV PATH="${VENV}/bin:$PATH"
+
 RUN apt-get update && apt-get -y upgrade && \
     apt-get -y install --no-install-recommends tabix liblzma-dev zlib1g-dev \
     r-base-core r-bioc-dnacopy && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-ENV VENV /opt/venv
-
-RUN python -m pip install --upgrade --no-cache-dir pip
-RUN python -m venv ${VENV}
-ENV PATH="${VENV}/bin:$PATH"
-
-RUN pip install --no-cache-dir --upgrade pip
-
-RUN pip install --no-cache-dir cnvkit==0.9.10
+RUN python -m pip install --upgrade --no-cache-dir pip && \
+    python -m venv ${VENV} && \
+    pip install --no-cache-dir "cnvkit==0.9.10" "numpy<2.0.0"
 
-RUN adduser --disabled-password --gecos '' ubuntu && \
-    chsh -s /bin/bash && mkdir -p /home/ubuntu
+RUN adduser --disabled-password --gecos "" ubuntu && \
+    chsh -s /bin/bash ubuntu && \
+    mkdir -p /home/ubuntu
 
 USER ubuntu
 WORKDIR /home/ubuntu

CHANGELOG.rst

@@ -23,7 +23,8 @@ Fixed:
 ^^^^^^
 * Corrected tool name in deduplication metrics https://github.com/Clinical-Genomics/BALSAMIC/pull/1441
 * MSI table https://github.com/Clinical-Genomics/BALSAMIC/pull/1459
-
+* Pin numpy version in CNVkit container https://github.com/Clinical-Genomics/BALSAMIC/pull/1457
+* CNVkit incorrect version in the documentation https://github.com/Clinical-Genomics/BALSAMIC/pull/1457
 
 [15.0.1]
 --------

docs/balsamic_methods.rst

@@ -17,7 +17,7 @@ Apart from the Vardict filters to report the variants, the called-variants were
 (*MQ >= 40, DP >= 100, VD >= 5, Minimum AF >= 0.007, Maximum AF < 1, GNOMADAF_popmax <= 0.005, swegen AF < 0.01*).
 Only those variants that fulfilled the filtering criteria and scored as `PASS` in the VCF file were reported.
 Structural variants (SV) were called using Manta v1.6.0 :superscript:`9` and Dellyv1.0.3 :superscript:`10`.
-Copy number variations (CNV) were called using CNVkit v0.9.9 :superscript:`11`.
+Copy number variations (CNV) were called using CNVkit v0.9.10 :superscript:`11`.
 The variant calls from CNVkit, Manta and Delly 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).
 All variants were annotated using Ensembl VEP v104.3 :superscript:`13`. We used vcfanno v0.3.3 :superscript:`14`

docs/bioinfo_softwares.rst

@@ -39,7 +39,7 @@ cnvkit
 ~~~~~~
 :Source code: `GitHub` `<https://github.com/etal/cnvkit>`_
 :Article: `PLOS Computational Biology` `<https://doi.org/10.1371/journal.pcbi.1004873>`_
-:Version: `0.9.9`
+:Version: `0.9.10`
 
 cnvpytor
 ~~~~~~~~

tests/test_data/config.json

@@ -200,7 +200,7 @@
   "bioinfo_tools_version": {
     "bcftools": ["1.15.1", "1.10.2", "1.9"],
     "tabix": ["1.11", "0.2.6"],
-    "cnvkit": ["0.9.9"],
+    "cnvkit": ["0.9.10"],
     "bwa": ["0.7.17"],
     "gatk": ["3.8"],
     "samtools": ["1.15.1", "1.9"],

tests/test_data/config_pon.json

@@ -56,7 +56,7 @@
     "sambamba": ["0.8.2"],
     "bcftools": ["1.9", "1.10.2", "1.15.1"],
     "tabix": ["0.2.6", "1.11"],
-    "cnvkit": ["0.9.9"],
+    "cnvkit": ["0.9.10"],
     "bedtools": ["2.30.0"],
     "ensembl-vep": ["104.3"],
     "vcfanno": ["0.3.3"],