From 0a4347d92dae73c8043ab1fea8c57c7ec98d4d79 Mon Sep 17 00:00:00 2001 From: EddieLF Date: Mon, 16 Feb 2026 15:05:13 +1100 Subject: [PATCH 1/2] Add worker_cores init_batch option for combiner --- src/cpg_seqr_loader/scripts/run_combiner.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/cpg_seqr_loader/scripts/run_combiner.py b/src/cpg_seqr_loader/scripts/run_combiner.py index d720c4b..902e380 100644 --- a/src/cpg_seqr_loader/scripts/run_combiner.py +++ b/src/cpg_seqr_loader/scripts/run_combiner.py @@ -45,6 +45,7 @@ def main( worker_memory=config.config_retrieve(['combiner', 'worker_memory']), driver_memory=config.config_retrieve(['combiner', 'driver_memory']), driver_cores=config.config_retrieve(['combiner', 'driver_cores']), + worker_cores=config.config_retrieve(['combiner', 'worker_cores']), ) # generate these in the job, instead of passing through From 56d93bdd9fd97f85a7348dcc4930d28f0540f959 Mon Sep 17 00:00:00 2001 From: EddieLF Date: Mon, 16 Feb 2026 15:05:18 +1100 Subject: [PATCH 2/2] =?UTF-8?q?Bump=20version:=200.1.15=20=E2=86=92=200.1.?= =?UTF-8?q?16?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- Dockerfile | 2 +- README.md | 4 ++-- pyproject.toml | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index 084a6ca..0b2492c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ FROM australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_hail_gcloud:0.2.137.cpg1-2 ENV PYTHONDONTWRITEBYTECODE=1 -ENV VERSION=0.1.15 +ENV VERSION=0.1.16 WORKDIR /cpg_seqr_loader diff --git a/README.md b/README.md index ac9d981..5d71eb4 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,7 @@ CPG-Flow workflows are operated entirely by defining input Cohorts (see [here](h ```bash analysis-runner \ --skip-repo-checkout \ - --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.15 \ + --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.16 \ --config src/cpg_seqr_loader/config_template.toml \ --config cohorts.toml \ # containing the inputs_cohorts and sequencing_type --dataset seqr \ @@ -70,7 +70,7 @@ analysis-runner \ ```bash analysis-runner \ --skip-repo-checkout \ - --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.15 \ + --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.16 \ --config src/cpg_seqr_loader/config_template.toml \ --config cohorts.toml \ # containing the inputs_cohorts and sequencing_type --dataset seqr \ diff --git a/pyproject.toml b/pyproject.toml index 90491e8..5e10e13 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ description='Seqr-Loader (gVCF-combiner) implemented in CPG-Flow' readme = "README.md" # currently cpg-flow is pinned to this version requires-python = ">=3.10,<3.12" -version="0.1.15" +version="0.1.16" license={"file" = "LICENSE"} classifiers=[ 'Environment :: Console', @@ -120,7 +120,7 @@ hail = ["hail"] "src/cpg_seqr_loader/scripts/annotate_cohort.py" = ["E501"] [tool.bumpversion] -current_version = "0.1.15" +current_version = "0.1.16" parse = "(?P\\d+)\\.(?P\\d+)\\.(?P\\d+)" serialize = ["{major}.{minor}.{patch}"] commit = true