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Merged
merged 3 commits into from
Jan 21, 2025
Merged

main <- Dev #1025

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a96e77f
add skip_check_sex_and_relatedness to pipeline-worker (#1023)
jklugherz Jan 21, 2025
da41e1c
update pipeline-runner helm release action to bump version too
jklugherz Jan 21, 2025
dfcc7c2
Merge pull request #1024 from broadinstitute/pipeline-runner-release
jklugherz Jan 21, 2025
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21 changes: 19 additions & 2 deletions .github/workflows/prod-release.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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1 change: 1 addition & 0 deletions v03_pipeline/api/model.py
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Expand Up @@ -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
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