Only show green genes as standard

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

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**

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 .
 ```
 
 ---

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"

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

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": {

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<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 commit = true

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/

src/talos/templates/index.html.jinja

@@ -152,17 +152,17 @@
                                 <label class="form-check-label" for="conf-3">🟢 Green</label>
                             </div>
                             <div class="form-check form-check-inline">
-                                <input class="form-check-input conf-filter" type="checkbox" id="conf-2" value="2" checked>
+                                <input class="form-check-input conf-filter" type="checkbox" id="conf-2" value="2">
                                 <label class="form-check-label" for="conf-2">🟡 Amber</label>
                             </div>
                         </div>
                         <div>
                             <div class="form-check form-check-inline">
-                                <input class="form-check-input conf-filter" type="checkbox" id="conf-1" value="1" checked>
+                                <input class="form-check-input conf-filter" type="checkbox" id="conf-1" value="1">
                                 <label class="form-check-label" for="conf-1">🔴 Red</label>
                             </div>
                             <div class="form-check form-check-inline">
-                                <input class="form-check-input conf-filter" type="checkbox" id="conf-0" value="0" checked>
+                                <input class="form-check-input conf-filter" type="checkbox" id="conf-0" value="0">
                                 <label class="form-check-label" for="conf-0">⚪ Unknown</label>
                             </div>
                         </div>

src/talos/version.py

@@ -1 +1 @@
-__version__ = '11.0.2'
+__version__ = '11.0.3'