Scheduled Run #12
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 | |
| 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' | |
| 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 mamba --only_fetch true --bioproject "PRJNA1102327" --outdir ${{ env.NXF_OUPUT }} | |
| - name: Split SRAs into chunks | |
| if: ${{ hashFiles('output/metadata/SraRunTable_PRJNA1102327_automated_new.txt') != '' }} | |
| id: split_sra | |
| run: | | |
| mkdir -p ${{ github.workspace }}/sra_chunks | |
| mv ${{ env.NXF_OUPUT }}/metadata/SraRunTable_PRJNA1102327_automated_new.txt ${{ github.workspace }}/sra_chunks/ | |
| split -l 5 ${{ github.workspace }}/sra_chunks/SraRunTable_PRJNA1102327_automated_new.txt ${{ github.workspace }}/sra_chunks/chunk_ | |
| rm ${{ github.workspace }}/sra_chunks/SraRunTable_PRJNA1102327_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_PRJNA1102327_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 mamba --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@v2 | |
| 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_PRJNA1102327_automated_updated.csv ${{ github.workspace }}/metadata/SraRunTable_PRJNA1102327_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_PRJNA1102327_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 |