Scheduled Run #218
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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: "24.10.3" | |
| NXF_WORK: ${{ github.workspace }}/work | |
| NXF_OUTPUT: ${{ github.workspace }}/outputs | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| FLUSRA_VERSION: 'main' | |
| FILES_PER_CHUNK: 5 | |
| BIOPROJECTS: "PRJNA1102327,PRJNA1122849" | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| fetch_sra: | |
| runs-on: ubuntu-24.04 | |
| outputs: | |
| chunk_files: ${{ steps.split_sra.outputs.chunk_files }} | |
| 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 --only_fetch true --bioproject ${{ env.BIOPROJECTS }} --outdir ${{ env.NXF_OUTPUT }} | |
| - name: Split SRAs into chunks | |
| if: ${{ hashFiles('outputs/metadata/SraRunTable_automated_new.txt') != '' }} | |
| id: split_sra | |
| run: | | |
| mkdir -p ${{ github.workspace }}/sra_chunks/ | |
| grep -vxFf ${{ env.NXF_OUTPUT }}/metadata/SraRunTable_automated_milk_samples.txt ${{ env.NXF_OUTPUT }}/metadata/SraRunTable_automated_new.txt > ${{ env.NXF_OUTPUT }}/metadata/SraRunTable_without_milk_samples.txt | |
| split -l ${{ env.FILES_PER_CHUNK }} ${{ env.NXF_OUTPUT }}/metadata/SraRunTable_without_milk_samples.txt ${{ github.workspace }}/sra_chunks/chunk_ | |
| split -l ${{ env.FILES_PER_CHUNK }} ${{ env.NXF_OUTPUT }}/metadata/SraRunTable_automated_milk_samples.txt ${{ github.workspace }}/sra_chunks/milk_chunk_ | |
| chunk_files=$(ls ${{ github.workspace }}/sra_chunks/ | jq -R . | jq -s . | tr -d '\n' | tr -d " ") | |
| echo "chunk_files=$chunk_files" >> $GITHUB_OUTPUT | |
| - name: Upload chunk files | |
| if: ${{ steps.split_sra.outputs.chunk_files != '' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: sra_chunks | |
| 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_OUTPUT }}/metadata/SraRunTable_automated_updated.csv | |
| - name: Upload Nextflow log | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-run-fetch-sra | |
| include-hidden-files: true | |
| path: | | |
| ${{ github.workspace }}/.nextflow.log | |
| process_sra: | |
| needs: fetch_sra | |
| if: ${{ needs.fetch_sra.outputs.chunk_files != '' }} | |
| runs-on: ubuntu-24.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| chunk_file: ${{fromJson(needs.fetch_sra.outputs.chunk_files)}} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Install Dependencies | |
| uses: ./.github/actions/install-dependencies | |
| - name: Download chunk files | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: sra_chunks | |
| path: ${{ github.workspace }}/sra_chunks/ | |
| - name: Setup samples | |
| run: | | |
| # if milk in chunk_file name, then set github env as IS_MILK_SAMPLE = true | |
| if [[ ${{ matrix.chunk_file }} == *"milk"* ]]; then | |
| echo "IS_MILK_SAMPLE=true" >> $GITHUB_ENV | |
| else | |
| echo "IS_MILK_SAMPLE=false" >> $GITHUB_ENV | |
| fi | |
| - name: Run nextflow | |
| if: ${{ env.IS_MILK_SAMPLE != 'true' }} | |
| run: nextflow run https://github.com/gp201/flusra.git -r ${{ env.FLUSRA_VERSION }} -c ${{ github.workspace }}/config/nextflow.config -profile mamba --sra_accessions ${{ github.workspace }}/sra_chunks/${{ matrix.chunk_file }} --outdir ${{ env.NXF_OUTPUT }} | |
| - name: Run nextflow for milk samples | |
| if: ${{ env.IS_MILK_SAMPLE == 'true' }} | |
| run: nextflow run https://github.com/gp201/flusra.git -r ${{ env.FLUSRA_VERSION }} -c ${{ github.workspace }}/config/nextflow.config -profile mamba --sra_accessions ${{ github.workspace }}/sra_chunks/${{ matrix.chunk_file }} --milk_sra_accessions ${{ github.workspace }}/sra_chunks/${{ matrix.chunk_file }} --outdir ${{ env.NXF_OUTPUT }} | |
| - name: Upload Outputs | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: files-${{ matrix.chunk_file }} | |
| path: | | |
| ${{ env.NXF_OUTPUT }}/fasta/ | |
| ${{ env.NXF_OUTPUT }}/depth/ | |
| ${{ env.NXF_OUTPUT }}/variants/ | |
| - name: Upload Demixed | |
| if: ${{ env.IS_MILK_SAMPLE == 'true' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: demixed-${{ matrix.chunk_file }} | |
| path: | | |
| ${{ env.NXF_OUTPUT }}/demixed/ | |
| - name: Upload Nextflow log | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-run-${{ matrix.chunk_file }} | |
| include-hidden-files: true | |
| path: | | |
| ${{ github.workspace }}/.nextflow.log | |
| push_files: | |
| needs: [process_sra] | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Download metadata | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: metadata | |
| path: ${{ env.NXF_OUTPUT }}/ | |
| - name: Download files | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: files-* | |
| path: ${{ env.NXF_OUTPUT }}/ | |
| merge-multiple: true | |
| - name: Download demixed files | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: demixed-* | |
| path: ${{ env.NXF_OUTPUT }}/demixed/ | |
| 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_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 |