Add SAM recommendation of MAPQ=0 for unmapped reads #83
Workflow file for this run
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: Handle PDF pull request | |
| on: | |
| pull_request: | |
| paths: '*.tex' | |
| jobs: | |
| LaTeX: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Identify changed LaTeX documents | |
| env: | |
| pr_number: ${{ github.event.number }} | |
| base_sha: ${{ github.event.pull_request.base.sha }} | |
| head_sha: ${{ github.event.pull_request.head.sha }} | |
| run: | | |
| mergebase_sha=$(git merge-base $base_sha $head_sha) | |
| echo "mergebase_sha=$mergebase_sha" >> $GITHUB_ENV | |
| changed=$(git diff-tree --name-only --merge-base $base_sha $head_sha -- '*.tex' | tr '\n' ' ') | |
| echo "changed=$changed" >> $GITHUB_ENV | |
| echo "pdfs=$(ls -1 $changed | sed 's,^,new/,;s,tex$,pdf,' | tr '\n' ' ')" >> $GITHUB_ENV | |
| echo "diffs=$(ls -1 $changed | sed 's,^,diff/,;s,tex$,pdf,' | tr '\n' ' ')" >> $GITHUB_ENV | |
| echo "pr_number=$pr_number" > environ.txt | |
| echo "base_sha=$base_sha" >> environ.txt | |
| echo "head_sha=$head_sha" >> environ.txt | |
| echo "mergebase_sha=$mergebase_sha" >> environ.txt | |
| - name: Run LaTeX | |
| uses: ./.github/actions/texlive | |
| if: ${{ env.changed }} | |
| with: | |
| run1: make ${{ env.pdfs }} | |
| run2: -make -k OLD=$mergebase_sha NEW=HEAD ${{ env.diffs }} | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: pdf | |
| retention-days: 1 | |
| if-no-files-found: ignore | |
| path: | | |
| environ.txt | |
| new/*.pdf | |
| diff/*.pdf |