📝 SNV HotSpot Updates #11
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Release Submodules Updater | |
| on: | |
| release: | |
| types: [published] | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| jobs: | |
| update-submodules: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: checkout-annot | |
| name: Checkout Annotation Repo | |
| uses: actions/checkout@v4 | |
| with: | |
| path: annotation | |
| submodules: true | |
| - id: checkout-somatic | |
| name: Checkout Somatic Repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: kids-first/kf-somatic-workflow | |
| path: somatic | |
| submodules: true | |
| - id: checkout-tumor-only | |
| name: Checkout Tumor Only Repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: kids-first/kf-tumor-workflow | |
| path: tumor-only | |
| submodules: true | |
| - id: checkout-germline | |
| name: Checkout Germline Repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: kids-first/kf-germline-workflow | |
| path: germline | |
| submodules: true | |
| - id: checkout-jg | |
| name: Checkout Joint Genotyping Repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: kids-first/kf-jointgenotyping-workflow | |
| path: joint-genotyping | |
| submodules: true | |
| - id: get-germline-annot-version | |
| name: Get Germline Annotation Workflow Version | |
| run: | | |
| GVERSION=$(yq '."sbg:links" | .[] | select(.label == "github-release") | .id | split("/") | .[-1]' ./annotation/workflows/kfdrc-germline-snv-annot-workflow.cwl) | |
| echo "GERMLINE_VERSION=$GVERSION" >> "$GITHUB_ENV" | |
| - id: get-somatic-annot-version | |
| name: Get Somatic Annotation Workflow Version | |
| run: | | |
| SVERSION=$(yq '."sbg:links" | .[] | select(.label == "github-release") | .id | split("/") | .[-1]' ./annotation/workflows/kfdrc-somatic-snv-annot-workflow.cwl) | |
| echo "SOMATIC_VERSION=$SVERSION" >> "$GITHUB_ENV" | |
| - id: update-germline-submodules | |
| name: Update Germline Submodules | |
| if: ${{ env.GERMLINE_VERSION == github.ref_name }} | |
| run: | | |
| cd germline | |
| git submodule update --remote --recursive kf-annotation-tools | |
| cd kf-annotation-tools | |
| git checkout $GITHUB_REF_NAME | |
| cd ../../joint-genotyping | |
| git submodule update --remote --recursive kf-annotation-tools | |
| cd kf-annotation-tools | |
| git checkout $GITHUB_REF_NAME | |
| - id: update-somatic-submodules | |
| name: Update Somatic Submodules | |
| if: ${{ env.SOMATIC_VERSION == github.ref_name }} | |
| run: | | |
| cd somatic | |
| git submodule update --remote --recursive kf-annotation-tools | |
| cd kf-annotation-tools | |
| git checkout $GITHUB_REF_NAME | |
| cd ../../tumor-only | |
| git submodule update --remote --recursive kf-annotation-tools | |
| cd kf-annotation-tools | |
| git checkout $GITHUB_REF_NAME | |
| - id: cpr-germline | |
| if: ${{ env.GERMLINE_VERSION == github.ref_name }} | |
| name: Germline PR | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ secrets.MIGBRO_GHA_PAT }} | |
| path: ./germline | |
| commit-message: ":robot: update annotation submodule" | |
| title: ":robot: Update Annotation Submodule for Release ${{ github.ref_name }}" | |
| body: | | |
| Automated changes by [create-pull-request](https://github.com/peter-evans/create-pull-request) GitHub action. | |
| Updates the annotation submodule in this repository for release ${{ github.ref_name }} | |
| delete-branch: true | |
| branch: annotation-submodule-to-${{ github.ref_name }} | |
| labels: bix-dev | |
| - id: cpr-joint-genotyping | |
| if: ${{ env.GERMLINE_VERSION == github.ref_name }} | |
| name: Joint Genotyping PR | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ secrets.MIGBRO_GHA_PAT }} | |
| path: ./joint-genotyping | |
| commit-message: ":robot: update annotation submodule" | |
| title: ":robot: Update Annotation Submodule for Release ${{ github.ref_name }}" | |
| body: | | |
| Automated changes by [create-pull-request](https://github.com/peter-evans/create-pull-request) GitHub action. | |
| Updates the annotation submodule in this repository for release ${{ github.ref_name }} | |
| delete-branch: true | |
| branch: annotation-submodule-to-${{ github.ref_name }} | |
| labels: bix-dev | |
| - id: cpr-somatic | |
| if: ${{ env.SOMATIC_VERSION == github.ref_name }} | |
| name: Somatic PR | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ secrets.MIGBRO_GHA_PAT }} | |
| path: ./somatic | |
| commit-message: ":robot: update annotation submodule" | |
| title: ":robot: Update Annotation Submodule for Release ${{ github.ref_name }}" | |
| body: | | |
| Automated changes by [create-pull-request](https://github.com/peter-evans/create-pull-request) GitHub action. | |
| Updates the annotation submodule in this repository for release ${{ github.ref_name }} | |
| delete-branch: true | |
| branch: annotation-submodule-to-${{ github.ref_name }} | |
| labels: bix-dev | |
| - id: cpr-tumor-only | |
| if: ${{ env.SOMATIC_VERSION == github.ref_name }} | |
| name: Tumor Only PR | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ secrets.MIGBRO_GHA_PAT }} | |
| path: ./tumor-only | |
| commit-message: ":robot: update annotation submodule" | |
| title: ":robot: Update Annotation Submodule for Release ${{ github.ref_name }}" | |
| body: | | |
| Automated changes by [create-pull-request](https://github.com/peter-evans/create-pull-request) GitHub action. | |
| Updates the annotation submodule in this repository for release ${{ github.ref_name }} | |
| delete-branch: true | |
| branch: annotation-submodule-to-${{ github.ref_name }} | |
| labels: bix-dev |