Update docs #98
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| # Workflow derived from https://github.com/r-lib/actions/tree/master/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master, wgbs] | |
| pull_request: | |
| branches: [main, master, wgbs] | |
| name: setup_camdac | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| extra-repositories: 'https://bioconductor.org/packages/3.16/bioc' | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| with: | |
| pandoc-version: '2.17.1' | |
| - run: echo "# Test | pandoc -t html" | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| error-on: '"error"' | |
| # pipeline_files: | |
| # needs: R-CMD-check | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| # R_KEEP_PKG_SOURCE: yes | |
| # steps: | |
| # - name: Cache pipeline files | |
| # id: cache-camdac | |
| # uses: actions/cache@v3 | |
| # env: | |
| # cache-name: cache-camdac | |
| # with: | |
| # path: pipeline_files | |
| # key: ${{ runner.os }}-camdac-${{ hashFiles('inst/extdata/pipeline_files_urls.txt') }} | |
| # restore-keys: | | |
| # ${{ runner.os }}-camdac-${{ env.cache-name }}- | |
| # - name: Load cached files | |
| # if: steps.cache-camdac.outputs.cache-hit != 'true' | |
| # run: | | |
| # echo "Downloading cache" | |
| # Rscript -e 'devtools::load_all();download_pipeline_files("wgbs", "./pipline_files/")' | |
| # Rscript -e 'devtools::load_all();download_pipeline_files("rrbs", "./pipline_files/")' | |
| # - name: Restore cached data | |
| # if: steps.cache-data-txt.outputs.cache-hit == 'true' | |
| # run: echo "Restoring cached data" |