Compile virion #729
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| name: Compile virion | |
| # Controls when the action will run. | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| # run once a week | |
| schedule: | |
| - cron: "0 0 * * *" | |
| workflow_dispatch: | |
| jobs: | |
| GenBank: | |
| runs-on: ubuntu-latest | |
| container: colebrookson/virion:latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: julia-actions/setup-julia@v1 | |
| with: | |
| version: 1.7 | |
| - name: Download GenBank | |
| run: | | |
| Rscript -e 'source("Code/02_1a_Download GenBank.R")' | |
| - name: Digest GenBank | |
| run: | | |
| Rscript -e 'source("Code/02_1b_Digest GenBank.R")' | |
| - name: Format GenBank | |
| run: | | |
| Rscript -e 'source("Code/02_1c_Format GenBank.R")' | |
| - name: Save artifacts | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: GenBankFormatted | |
| path: Intermediate/Formatted/GenbankFormatted.csv.gz | |
| Globi: | |
| runs-on: ubuntu-latest | |
| container: colebrookson/virion:latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download Globi | |
| run: | | |
| Rscript -e 'source("Code/02_3a_Download GLOBI.R")' | |
| - name: Digest Globi | |
| run: | | |
| Rscript -e 'source("Code/02_3b_Digest GLOBI.R")' | |
| - name: Format Globi | |
| run: | | |
| Rscript -e 'source("Code/02_3c_Format GLOBI.R")' | |
| - name: Save artifacts | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: GlobiFormatted | |
| path: Intermediate/Formatted/GLOBIFormatted.csv | |
| Finish: | |
| runs-on: ubuntu-latest | |
| container: colebrookson/virion:latest | |
| needs: [GenBank, Globi] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Get GenBank | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: GenBankFormatted | |
| - name: Get Globi | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: GlobiFormatted | |
| - name: Merge clean files | |
| run: | | |
| Rscript -e 'source("Code/03_Merge clean files.R")' | |
| - name: High level checks | |
| run: | | |
| Rscript -e 'source("Code/04_High level VIRION checks.R")' | |
| - name: Dissolve VIRION | |
| run: | | |
| Rscript -e 'source("Code/05_Dissolve VIRION.R")' | |
| - name: Save the artifacts | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: VIRION | |
| path: Virion | |
| - name: Deploy | |
| uses: JamesIves/github-pages-deploy-action@4.1.7 | |
| with: | |
| branch: gh-pages # The branch the action should deploy to. | |
| folder: Virion # The folder the action should deploy. |