🐛 Fix bugs introduced from tool refactor #9
Workflow file for this run
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| 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 | |
| - 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 |