Routine Processing #3
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: 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' | |
| concurrency: | |
| group: ${{ github.repository }} | |
| env: | |
| NXF_VER: "24.10.3" | |
| NXF_WORK: ${{ github.workspace }}/work | |
| NXF_OUTPUT: ${{ github.workspace }}/outputs | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| FLUSRA_VERSION: 'main' | |
| BIOPROJECTS: "PRJNA1102327,PRJNA1122849,PRJNA1134696" | |
| TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| defaults: | |
| run: | |
| shell: bash -el {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 ${{ env.NXF_OUTPUT }} -name GitHub_$(date +%Y-%m-%d) -with-tower -latest | |
| - name: Push outputs | |
| 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 }}/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/*.fa | |
| git add ${{ github.workspace }}/depth/*.tsv | |
| git add ${{ github.workspace }}/variants/*.tsv | |
| git commit -m "Add consensus sequences, depth, variant files, demixed files and updated metadata" | |
| git push | |
| - name: Upload Nextflow log | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-run-${{ matrix.chunk_file }} | |
| include-hidden-files: true | |
| path: | | |
| ${{ github.workspace }}/.nextflow.log |