From a96e77fb20224d8f41490c32d89d2daa5c7d6655 Mon Sep 17 00:00:00 2001 From: Julia Klugherz Date: Tue, 21 Jan 2025 11:03:20 -0500 Subject: [PATCH 1/2] add skip_check_sex_and_relatedness to pipeline-worker (#1023) --- v03_pipeline/api/model.py | 1 + 1 file changed, 1 insertion(+) diff --git a/v03_pipeline/api/model.py b/v03_pipeline/api/model.py index 4e2f1cd71..b8a942e61 100644 --- a/v03_pipeline/api/model.py +++ b/v03_pipeline/api/model.py @@ -14,6 +14,7 @@ class LoadingPipelineRequest(BaseModel): dataset_type: DatasetType ignore_missing_samples_when_remapping: bool = False skip_validation: bool = False + skip_check_sex_and_relatedness: bool = False @field_validator('callset_path') @classmethod From da41e1cea7cad6ae49f25482704536920d913e2e Mon Sep 17 00:00:00 2001 From: Julia Klugherz Date: Tue, 21 Jan 2025 11:32:51 -0500 Subject: [PATCH 2/2] update pipeline-runner helm release action to bump version too --- .github/workflows/prod-release.yml | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/.github/workflows/prod-release.yml b/.github/workflows/prod-release.yml index d67f37df3..b5ac42431 100644 --- a/.github/workflows/prod-release.yml +++ b/.github/workflows/prod-release.yml @@ -86,11 +86,28 @@ jobs: persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token fetch-depth: 0 # otherwise, you will failed to push refs to dest repo - - name: Update appVersion in seqr Chart file + - name: Get latest pipeline-runner version uses: mikefarah/yq@v4.22.1 + id: current with: cmd: > - yq -i '.appVersion = "${{ github.event.workflow_run.head_sha }}"' charts/pipeline-runner/Chart.yaml + yq -r '.version' charts/pipeline-runner/Chart.yaml + + - name: Bump version + id: bump + uses: cbrgm/semver-bump-action@main + with: + current-version: ${{ steps.current.outputs.result }} + bump-level: minor + + - name: Update appVersion and version in pipeline-runner Chart file + uses: mikefarah/yq@v4.22.1 + with: + cmd: > + yq -i ' + .appVersion = "${{ github.event.workflow_run.head_sha }}" | + .version = "${{ steps.bump.outputs.new_version }}" + ' charts/pipeline-runner/Chart.yaml - name: Commit and Push changes uses: Andro999b/push@v1.3