Compile virion #760
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: 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. |