👨🔬 Beta Workflow to Modify Ploidy #38
Workflow file for this run
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| name: Update Docker Tables | |
| on: [pull_request] | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| jobs: | |
| update-tables: | |
| name: Update Docker Tables | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - id: checkout | |
| uses: actions/checkout@v3 | |
| name: Checkout Repo | |
| with: | |
| ref: ${{ github.head_ref }} | |
| - id: make-bwagatk-alignment-table | |
| name: Make Docker Table for BWA/GATK Alignment Workflow | |
| run: | | |
| python .github/scripts/workflow_to_docker_table.py --output_file docs/dockers_bwagatk_alignment.md workflows/kfdrc_alignment_wf.cwl | |
| - id: make-gatk-cramtogvcf-table | |
| name: Make Docker Table for GATK CRAM to gVCF Workflow | |
| run: | | |
| python .github/scripts/workflow_to_docker_table.py --output_file docs/dockers_gatk_cramtogvcf.md workflows/kfdrc-gatk-haplotypecaller-wf.cwl | |
| - id: make-sentieon-alignment-table | |
| name: Make Docker Table for Sentieon Alignment Workflow | |
| run: | | |
| python .github/scripts/workflow_to_docker_table.py --output_file docs/dockers_sentieon_alignment.md workflows/kfdrc_sentieon_alignment_wf.cwl | |
| - id: make-sentieon-gvcf-table | |
| name: Make Docker Table for Sentieon gVCF Workflow | |
| run: | | |
| python .github/scripts/workflow_to_docker_table.py --output_file docs/dockers_sentieon_gvcf.md workflows/kfdrc_sentieon_gvcf_wf.cwl | |
| - id: cpr | |
| name: Create Pull Request | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| commit-message: update docker table | |
| title: Update Production WF Docker Tables | |
| body: | | |
| Automated changes by [create-pull-request](https://github.com/peter-evans/create-pull-request) GitHub action. | |
| Docker tables for production workflows now have most up-to-date and complete list of Dockers. | |
| delete-branch: true | |
| branch: ${{ github.head_ref }}-adjust-dockers | |
| labels: bix-dev |