Scheduled Run #186
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| name: Process Flu SRA | |
| run-name: ${{ github.event.inputs.reason || 'Scheduled Run' }} | |
| on: | |
| schedule: | |
| - cron: '0 17 * * *' | |
| workflow_dispatch: | |
| inputs: | |
| reason: | |
| description: 'Reason for running the workflow' | |
| required: true | |
| default: 'Routine Processing' | |
| concurrency: | |
| group: ${{ github.repository }} | |
| env: | |
| NXF_VER: "23.04.1" | |
| NXF_WORK: ${{ github.workspace }}/work | |
| NXF_OUPUT: ${{ github.workspace }}/output | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| fetch_sra: | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| chunk_files: ${{ steps.split_sra.outputs.chunk_files }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| 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 'main' -c ${{ github.workspace }}/config/nextflow.config -profile conda --only_fetch true --bioproject "PRJNA1102327,PRJNA1122849" --outdir ${{ env.NXF_OUPUT }} | |
| - name: Split SRAs into chunks | |
| if: ${{ hashFiles('output/metadata/SraRunTable_automated_new.txt') != '' }} | |
| id: split_sra | |
| run: | | |
| mkdir -p ${{ github.workspace }}/sra_chunks | |
| mv ${{ env.NXF_OUPUT }}/metadata/SraRunTable_automated_new.txt ${{ github.workspace }}/sra_chunks/ | |
| split -l 5 ${{ github.workspace }}/sra_chunks/SraRunTable_automated_new.txt ${{ github.workspace }}/sra_chunks/chunk_ | |
| rm ${{ github.workspace }}/sra_chunks/SraRunTable_automated_new.txt | |
| ls ${{ github.workspace }}/sra_chunks/ > chunk_files.txt | |
| chunk_files=$(cat chunk_files.txt | jq -R . | jq -s . | tr -d '\n' | tr -d " ") | |
| echo "chunk_files=$chunk_files" >> $GITHUB_OUTPUT | |
| - name: Upload chunk files | |
| if: ${{ steps.split_sra.outputs.chunk_files != '' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: chunk_files | |
| path: ${{ github.workspace }}/sra_chunks/ | |
| - name: Upload Metadata | |
| if: ${{ steps.split_sra.outputs.chunk_files != '' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: metadata | |
| path: ${{ env.NXF_OUPUT }}/metadata/SraRunTable_automated_updated.csv | |
| process_sra: | |
| needs: fetch_sra | |
| if: ${{ needs.fetch_sra.outputs.chunk_files != '' }} | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| chunk_file: ${{fromJson(needs.fetch_sra.outputs.chunk_files)}} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - uses: ./.github/actions/install-dependencies | |
| - name: Download chunk files | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: chunk_files | |
| path: ${{ github.workspace }}/sra_chunks/ | |
| - name: Run nextflow | |
| run: nextflow run https://github.com/gp201/flusra.git -r 'main' -c ${{ github.workspace }}/config/nextflow.config -profile conda --sra_accessions ${{ github.workspace }}/sra_chunks/${{ matrix.chunk_file }} --outdir ${{ env.NXF_OUPUT }} | |
| - name: Upload Metadata | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: files-${{ matrix.chunk_file }} | |
| path: | | |
| ${{ env.NXF_OUPUT }}/fasta/ | |
| ${{ env.NXF_OUPUT }}/depth/ | |
| ${{ env.NXF_OUPUT }}/variants/ | |
| - name: Upload Artifacts | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: outputs | |
| path: | | |
| /home/runner/ncbi_error_report.txt | |
| push_files: | |
| needs: process_sra | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Download metadata | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: metadata | |
| path: ${{ env.NXF_OUPUT }}/ | |
| - name: Download files | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: files-* | |
| path: ${{ env.NXF_OUPUT }}/ | |
| merge-multiple: true | |
| - 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_OUPUT }}/SraRunTable_automated_updated.csv ${{ github.workspace }}/metadata/SraRunTable_automated.csv | |
| mv ${{ env.NXF_OUPUT }}/fasta/*.fa ${{ github.workspace }}/fasta/ | |
| mv ${{ env.NXF_OUPUT }}/depth/*.tsv ${{ github.workspace }}/depth/ | |
| mv ${{ env.NXF_OUPUT }}/variants/*.tsv ${{ github.workspace }}/variants/ | |
| 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 and variants files and update metadata" | |
| git push |