Scheduled Run #42
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| name: Process Flu SRA (self-hosted) | |
| run-name: ${{ github.event.inputs.reason || 'Scheduled Run' }} | |
| on: | |
| schedule: | |
| - cron: '0 1 * * *' | |
| workflow_dispatch: | |
| inputs: | |
| reason: | |
| description: 'Reason for running the workflow' | |
| required: true | |
| default: 'Routine Processing' | |
| testing: | |
| type: boolean | |
| description: 'Run in testing mode' | |
| concurrency: | |
| group: ${{ github.repository }} | |
| env: | |
| NXF_VER: "24.10.4" | |
| NXF_WORK: ${{ github.workspace }}/work | |
| NXF_OUTPUT: ${{ github.workspace }}/outputs | |
| NXF_NAME: github-${{ github.run_number }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| FLUSRA_VERSION: 'main' | |
| BIOPROJECTS: "PRJNA1102327,PRJNA1122849,PRJNA1134696" | |
| TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| TOWER_WORKSPACE_ID: ${{ secrets.TOWER_WORKSPACE_ID }} | |
| defaults: | |
| run: | |
| shell: bash -eli {0} | |
| jobs: | |
| process_sra: | |
| runs-on: self-hosted | |
| permissions: | |
| contents: write | |
| id-token: write | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - uses: ./.github/actions/install-dependencies | |
| - name: Run nextflow | |
| run: nextflow run https://github.com/gp201/flusra.git -r ${{ env.FLUSRA_VERSION }} -c ${{ github.workspace }}/config/nextflow.config -profile mamba --bioproject ${{ env.BIOPROJECTS }} --outdir ${{ env.NXF_OUTPUT }} -name ${{ env.NXF_NAME }} -with-tower -latest | |
| - name: Push outputs | |
| if: ${{ hashFiles('outputs/metadata/*.tsv') != '' }} | |
| run: | | |
| git config --global user.email "github-actions[bot]@users.noreply.github.com" | |
| git config --global user.name "github-actions[bot]" | |
| mv ${{ env.NXF_OUTPUT }}/metadata/SraRunTable_automated_updated.csv ${{ github.workspace }}/metadata/SraRunTable_automated.csv | |
| mv ${{ env.NXF_OUTPUT }}/fasta/*.fa ${{ github.workspace }}/fasta/ | |
| mv ${{ env.NXF_OUTPUT }}/depth/*.tsv ${{ github.workspace }}/depth/ | |
| mv ${{ env.NXF_OUTPUT }}/variants/*.tsv ${{ github.workspace }}/variants/ | |
| if [ -d ${{ env.NXF_OUTPUT }}/demixed/ ]; then | |
| mv ${{ env.NXF_OUTPUT }}/demixed/* ${{ github.workspace }}/demixed/ | |
| git add ${{ github.workspace }}/demixed/ | |
| fi | |
| git add ${{ github.workspace }}/metadata/SraRunTable_automated.csv | |
| git add ${{ github.workspace }}/fasta/ | |
| git add ${{ github.workspace }}/depth/ | |
| git add ${{ github.workspace }}/variants/ | |
| git commit -m "Add consensus sequences, depth, variant files, demixed files and updated metadata" | |
| - name: Push to GitHub | |
| if: ${{ github.event.inputs.testing != 'true' || github.event_name == 'schedule' }} | |
| run: git push | |
| - name: Generate Run Summary | |
| if: ${{ hashFiles('outputs/metadata/*.tsv') != '' }} | |
| run: | | |
| echo "# Job Summary $(date)" >> $GITHUB_STEP_SUMMARY | |
| echo "## Job Information" >> $GITHUB_STEP_SUMMARY | |
| samples=$(awk -F'\t' '$2 == "True" { print $1 }' outputs/metadata/*_to_process.tsv) | |
| milk=$(awk -F"\t" '$3 == "True" { print $1 }' outputs/metadata/*_to_process.tsv) | |
| echo "<details><summary>Processed $(echo "$samples" | wc -l) samples</summary>" >> $GITHUB_STEP_SUMMARY | |
| printf '%s\n' "$samples" >> $GITHUB_STEP_SUMMARY | |
| echo "</details>" >> $GITHUB_STEP_SUMMARY | |
| echo "<details><summary>Processed $(echo "$milk" | wc -l) milk samples</summary>" >> $GITHUB_STEP_SUMMARY | |
| printf '%s\n' "$milk" >> $GITHUB_STEP_SUMMARY | |
| echo "</details>" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "## Workflow diagram" >> $GITHUB_STEP_SUMMARY | |
| echo "\`\`\`mermaid" >> $GITHUB_STEP_SUMMARY | |
| cat outputs/pipeline_info/*.mmd >> $GITHUB_STEP_SUMMARY | |
| echo "\`\`\`" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| - name: Upload Nextflow log | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-run-log | |
| include-hidden-files: true | |
| path: ${{ github.workspace }}/.nextflow.log | |
| - name: Clean Nextflow Run | |
| if: success() | |
| run: nextflow clean $NXF_NAME -f |