diff --git a/Dockerfile b/Dockerfile index 957306e2..e46962c3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -61,7 +61,7 @@ COPY --from=bcftools_compiler /bcftools_install/usr/local/lib/ /usr/local/lib/ RUN ldconfig ARG ECHTVAR_VERSION=v0.2.2 -ARG VERSION=11.0.2 +ARG VERSION=11.0.3 RUN wget -q -O /bin/echtvar "https://github.com/brentp/echtvar/releases/download/${ECHTVAR_VERSION}/echtvar" && \ chmod +x /bin/echtvar diff --git a/README.md b/README.md index b5a08c44..50076a0d 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ There are two primary workflows: To build the Docker image: ``` -docker build -t talos:11.0.2 . +docker build -t talos:11.0.3 . ``` ### **2. Download Annotation Resources** diff --git a/docs/getting-started.md b/docs/getting-started.md index 9fa1ca0e..7e29b012 100644 --- a/docs/getting-started.md +++ b/docs/getting-started.md @@ -25,7 +25,7 @@ You will need: Build the Talos Docker image locally: ```bash -docker build -t talos:11.0.2 . +docker build -t talos:11.0.3 . ``` --- diff --git a/nextflow.config b/nextflow.config index 2f745b4b..434e4a32 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,8 +16,8 @@ params { large_files = "large_files" ref_genome = "${params.large_files}/ref.fa" - // Docker container - "docker build -t talos:11.0.2 ." - container = 'talos:11.0.2' + // Docker container - "docker build -t talos:11.0.3 ." + container = 'talos:11.0.3' // MANE transcript resource mane = "${params.large_files}/MANE.GRCh38.v1.5.summary.txt.gz" diff --git a/nextflow/inputs/config.toml b/nextflow/inputs/config.toml index e2554b4a..f01bb6c4 100644 --- a/nextflow/inputs/config.toml +++ b/nextflow/inputs/config.toml @@ -10,7 +10,7 @@ forced_panels = [ 144, 239] # 3 = Green only # 2 = Amber or Green only # 1 = Red, Amber, or Green -confidence_level = 3 +confidence_level = 1 [[GeneratePanelData.manual_overrides]] # this section permits the manual addition of genes to the panel data diff --git a/nextflow_schema.json b/nextflow_schema.json index 92600956..2cf64099 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -33,7 +33,7 @@ }, "container": { "type": "string", - "default": "talos:11.0.2", + "default": "talos:11.0.3", "description": "Docker container used by processes." }, "mane": { diff --git a/pyproject.toml b/pyproject.toml index d9d4667c..a469abea 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "hatchling.build" name='talos' description='Centre for Population Genomics Variant Prioritisation' readme = "README.md" -version="11.0.2" +version="11.0.3" requires-python = ">=3.10,<3.12" license-files = ["LICENSE"] classifiers=[ @@ -127,7 +127,7 @@ hail = ["hail", "hailtop"] "test/test_cpg_flow_utils.py" = ['ANN202', 'ARG001'] [tool.bumpversion] -current_version = "11.0.2" +current_version = "11.0.3" parse = "(?P\\d+)\\.(?P\\d+)\\.(?P\\d+)" serialize = ["{major}.{minor}.{patch}"] commit = true diff --git a/src/talos/cpg_internal_scripts/CPG_Dockerfile b/src/talos/cpg_internal_scripts/CPG_Dockerfile index 24475cfb..e01bd3ff 100644 --- a/src/talos/cpg_internal_scripts/CPG_Dockerfile +++ b/src/talos/cpg_internal_scripts/CPG_Dockerfile @@ -16,7 +16,7 @@ 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 11.0.2, Talos is building BCFtools from a private fork. This fork contains a single change - csq applies annotations +# AS OF 11.0.3, 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. @@ -53,7 +53,7 @@ RUN apt-get update && apt-get install --no-install-recommends -y \ FROM base AS talos ARG ECHTVAR_VERSION=v0.2.2 -ARG VERSION=11.0.2 +ARG VERSION=11.0.3 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/ diff --git a/src/talos/templates/index.html.jinja b/src/talos/templates/index.html.jinja index 63bc27c4..c6b7400d 100644 --- a/src/talos/templates/index.html.jinja +++ b/src/talos/templates/index.html.jinja @@ -152,17 +152,17 @@
- +
- +
- +
diff --git a/src/talos/version.py b/src/talos/version.py index 6b49d906..d1bb7002 100644 --- a/src/talos/version.py +++ b/src/talos/version.py @@ -1 +1 @@ -__version__ = '11.0.2' +__version__ = '11.0.3'