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Merged
MattWellie merged 1 commit into from
Jul 17, 2026
Merged

revert to reliance on canon bcftools #686

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14 changes: 12 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -17,6 +17,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
<!--changelog-start-->
<!--latest-start-->

[11.1.0] - 2026-07

### Removed

* All references to the private build of BCFtools. the `--greedy` behaviour is now released as standard in BCFtools 1.24

### Added

* STR functionality!

<!--latest-end-->

[11.0.0] - 2026-05-15

### Added
Expand Down Expand Up @@ -49,8 +61,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

> NOTE! For existing Talos users, obtaining this extra annotation will require the re-run of the annotation workflow. One example gene which is known to be obscured by this default behaviour was RNU2-2, but there may be others.

<!--latest-end-->

[10.0.1] - 2026-03-23

### Fixed
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32 changes: 9 additions & 23 deletions Dockerfile
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Expand Up @@ -19,46 +19,32 @@ RUN apt-get update && apt-get install -y --no-install-recommends \

FROM base AS bcftools_compiler

ARG BCFTOOLS_VERSION=1.23.1

# AS OF 11.0.0, Talos is building BCFtools from a private fork. This fork contains a single change - csq applies annotations
# to both coding and non-coding genes in the event of overlapping genes. By default BCFtools skips non-coding gene annotation
# if a coding transcript consequence was detected, but in practice this is masking clinically relevant non-coding gene variation
# in cases where the non-coding gene overlaps with a non-clinically relevant coding gene.
# The change made is to always search for non-coding variation, but to mask non-coding consequences in otherwise coding transcripts
# if a coding change was already detected.
ARG BCFTOOLS_VERSION=1.24

RUN apt-get update && apt-get install --no-install-recommends -y \
autoconf \
gcc \
git \
libbz2-dev \
libcurl4-openssl-dev \
liblzma-dev \
libssl-dev \
make \
zlib1g-dev && \
wget https://github.com/samtools/htslib/releases/download/${BCFTOOLS_VERSION}/htslib-${BCFTOOLS_VERSION}.tar.bz2 && \
tar -xf htslib-${BCFTOOLS_VERSION}.tar.bz2 && \
cd htslib-${BCFTOOLS_VERSION} && \
./configure --enable-libcurl && \
make && \
make DESTDIR=/bcftools_install install && \
cd .. && \
git clone https://github.com/populationgenomics/bcftools.git && \
cd bcftools && \
autoheader && \
autoconf && \
rm -rf /var/lib/apt/lists/* && \
wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
tar -xf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
cd bcftools-${BCFTOOLS_VERSION} && \
./configure --enable-libcurl --enable-s3 --enable-gcs && \
make && \
strip bcftools plugins/*.so && \
make DESTDIR=/bcftools_install install && \
cd htslib-${BCFTOOLS_VERSION} && \
make && \
make DESTDIR=/bcftools_install install

FROM base AS talos

COPY --from=bcftools_compiler /bcftools_install/usr/local/bin/* /usr/local/bin/
COPY --from=bcftools_compiler /bcftools_install/usr/local/libexec/bcftools/* /usr/local/libexec/bcftools/
COPY --from=bcftools_compiler /bcftools_install/usr/local/lib/ /usr/local/lib/
RUN ldconfig

ARG ECHTVAR_VERSION=v0.2.2
ENV VERSION=11.1.0
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1 change: 1 addition & 0 deletions nextflow/modules/annotation/AnnotateCsqWithBcftools/main.nf
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Expand Up @@ -14,6 +14,7 @@ process AnnotateCsqWithBcftools {
set -euo pipefail

bcftools csq --force -f "${reference}" \
--greedy 1 \
--local-csq \
-g ${gff3} \
--unify-chr-names 'chr,-,chr' \
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30 changes: 8 additions & 22 deletions src/talos/cpg_internal_scripts/CPG_Dockerfile
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Expand Up @@ -14,40 +14,26 @@ RUN apt-get update && apt-get install -y --no-install-recommends \

FROM base AS bcftools_compiler

# BCFtools 1.22+ doesn't do any inference on chr-prefixes during CSQ, so the mismatch between fasta/vcf, and the gff3 (no chr-prefix) needs to be handled explicitly
# BCFtools >=1.22 is required internally as it's the first version with a built-in Mitochondrial lookup table.
# AS OF 11.0.0, Talos is building BCFtools from a private fork. This fork contains a single change - csq applies annotations
# to both coding and non-coding genes in the event of overlapping genes. By default BCFtools skips non-coding gene annotation
# if a coding transcript consequence was detected, but in practice this is masking clinically relevant non-coding gene variation
# in cases where the non-coding gene overlaps with a non-clinically relevant coding gene.
# The change made is to always search for non-coding variation, but to mask non-coding consequences in otherwise coding transcripts
# if a coding change was already detected.
ARG BCFTOOLS_VERSION=1.23.1
ARG BCFTOOLS_VERSION=1.24

RUN apt-get update && apt-get install --no-install-recommends -y \
autoconf \
gcc \
git \
libbz2-dev \
libcurl4-openssl-dev \
liblzma-dev \
libssl-dev \
make \
zlib1g-dev && \
wget https://github.com/samtools/htslib/releases/download/${BCFTOOLS_VERSION}/htslib-${BCFTOOLS_VERSION}.tar.bz2 && \
tar -xf htslib-${BCFTOOLS_VERSION}.tar.bz2 && \
cd htslib-${BCFTOOLS_VERSION} && \
./configure --enable-libcurl && \
make && \
make DESTDIR=/bcftools_install install && \
cd .. && \
git clone https://github.com/populationgenomics/bcftools.git && \
cd bcftools && \
autoheader && \
autoconf && \
rm -rf /var/lib/apt/lists/* && \
wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
tar -xf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
cd bcftools-${BCFTOOLS_VERSION} && \
./configure --enable-libcurl --enable-s3 --enable-gcs && \
make && \
strip bcftools plugins/*.so && \
make DESTDIR=/bcftools_install install && \
cd htslib-${BCFTOOLS_VERSION} && \
make && \
make DESTDIR=/bcftools_install install

FROM base AS talos
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1 change: 1 addition & 0 deletions src/talos/cpg_internal_scripts/cpgflow_jobs/annotate_csq_with_bcftools.py
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Expand Up @@ -44,6 +44,7 @@ def make_bcftools_anno_jobs(
f"""
bcftools index -t {local_vcf}
bcftools csq --force -f {fasta} \\
--greedy 1 \\
--local-csq \\
--threads 4 \\
-g {gff3_file} \\
Expand Down
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