Ncbench #2
Workflow file for this run
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| name: NCBench Zenodo Upload | |
| # This workflow can be triggered manually with the GitHub actions workflow dispatch button. | |
| on: | |
| # upload can only be triggered manually for now | |
| workflow_dispatch: | |
| inputs: | |
| germline_wes: | |
| description: "Trigger NCBench upload" | |
| type: boolean | |
| default: true | |
| pull_request: | |
| jobs: | |
| ncbench-upload: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - profile: germline_wes | |
| enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline_wes ) }} | |
| env: | |
| pipeline_version: 3.2.3 | |
| steps: | |
| - name: Download files from AWS | |
| uses: keithweaver/[email protected] | |
| if: ${{ matrix.enabled }} | |
| with: | |
| revision: ${{ github.sha }} | |
| source: s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-59026dc07633edb83aab3bfb2f65f79db38437a1/test_full/variant_calling/strelka/ | |
| command: sync | |
| destination: ./variant_calling | |
| flags: --no-sign-request --include ".vcf.gz" --exclude "g.vcf.gz" | |
| - name: Download metadata file for Zenodo | |
| uses: actions/checkout@v4 | |
| with: | |
| sparse-checkout: | | |
| assets/zenodo_ncbench.json | |
| sparse-checkout-cone-mode: false | |
| - name: Create new Zenodo entry | |
| uses: popperized/zenodo/create@master | |
| env: | |
| ZENODO_METADATA_PATH: assets/zenodo_ncbench.json | |
| with: | |
| secrets: ${{ secrets.ZENODO_API_TOKEN }} | |
| - name: Upload file to Zenodo | |
| uses: popperized/zenodo/upload@master | |
| env: | |
| ZENODO_DEPOSIT_ID: #TODO get the dposit ID from the previous step | |
| ZENODO_UPLOAD_PATH: ./variant_calling_v$pipeline_version | |
| ZENODO_USE_SANDBOX: true | |
| with: | |
| secrets: ${{ secrets.ZENODO_API_TOKEN }} | |
| # - name: Install jq | |
| # uses: sergeysova/jq-action@v2 | |
| # - name: NCBench set config | |
| # uses: actions/checkout@v4 | |
| # with: | |
| # repository: FriederikeHanssen/ncbench | |
| # path: ncbench | |
| # ref: main | |
| # token: ${{ github.token }} | |
| # sparse-checkout: | | |
| # config/config.yaml | |
| # sparse-checkout-cone-mode: false | |
| # run: | | |
| # jq --help >> config.yaml | |
| # with: | |
| # repository: github.com/FriederikeHanssen/ncbench | |
| # path: ncbench | |
| # ref: main | |
| # TODO: how to retrieve the pipeline and tool versions | |
| # TODO: how to get the zenodo id | |
| #run: | | |
| # jq --version | |
| # git checkout -b ${{ github.sha }} | |
| # echo " nf-core-sarek-$pipeline_version-deepvariants-agilent-200M:" >> config.yaml | |
| # echo " labels:" >> config.yaml | |
| # echo " site: nf-core" >> config.yaml | |
| # echo " pipeline: nf-core/sarek v$" >> config.yaml | |
| # echo " trimming: Fastp v0.23." >> config.yaml | |
| # echo " read-mapping: bwa mem v0.7." >> config.yaml | |
| # echo " base-quality-recalibration: gatk4 v4.4.0." >> config.yaml | |
| # echo " realignment: " >> config.yaml | |
| # echo " variant-detection: deepvariant v1.5." >> config.yaml | |
| # echo " genotyping: " >> config.yaml | |
| # echo " reads: " >> config.yaml | |
| # echo " subcategory: NA12878-agilent" >> config.yaml | |
| # echo " zenodo:" >> config.yaml | |
| # echo " deposition: ?" >> config.yaml | |
| # echo " filename: nf-core-sarek-$pipeline_version/deepvariant/NA12878_200M/NA12878_200M.deepvariant.vcf." >> config.yaml | |
| # echo " benchmark: giab-NA12878-agilent-" >> config.yaml | |
| # echo " rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt" >> config.yaml | |
| # git config user.name github-actions | |
| # git config user.email [email protected] | |
| # git add . | |
| # git commit -m "Benchmarking ${{ github.sha }}" | |
| # git push origin ${{ github.sha }} | |
| # TB-sarek311-freebayes-agilent-200M: | |
| # labels: | |
| # site: TB QBiC | |
| # pipeline: nf-core/sarek v3.1.1 | |
| # trimming: Fastp v0.23.2 | |
| # read-mapping: bwa mem v0.7.17 | |
| # base-quality-recalibration: gatk4 v4.3.0.0 | |
| # realignment: none | |
| # variant-detection: freebayes v1.3.6 | |
| # genotyping: none | |
| # reads: 200M | |
| # subcategory: NA12878-agilent | |
| # zenodo: | |
| # deposition: 7376244 | |
| # filename: WES_agilent_high_cov_sarek311_NA12878_freebayes.vcf.gz | |
| # benchmark: giab-NA12878-agilent-200M | |
| # rename-contigs: resources/rename-contigs/ucsc-to-ensemb | |
| # TB-sarek311-haplotypecaller-agilent-200M: | |
| # labels: | |
| # site: TB QBiC | |
| # pipeline: nf-core/sarek v3.1.1 | |
| # trimming: Fastp v0.23.2 | |
| # read-mapping: bwa mem v0.7.17 | |
| # base-quality-recalibration: gatk4 v4.3.0.0 | |
| # realignment: none | |
| # variant-detection: gatk-haplotypecaller v4.3.0.0 | |
| # genotyping: none | |
| # reads: 200M | |
| # subcategory: NA12878-agilent | |
| # zenodo: | |
| # deposition: 7376244 | |
| # filename: WES_agilent_high_cov_sarek311_NA12878_haplotypecaller.vcf.gz | |
| # benchmark: giab-NA12878-agilent-200M | |
| # rename-contigs: resources/rename-contigs/ucsc-to-ensemb | |
| # TB-sarek311-strelka-agilent-200M: | |
| # labels: | |
| # site: TB QBiC | |
| # pipeline: nf-core/sarek v3.1.1 | |
| # trimming: Fastp v0.23.2 | |
| # read-mapping: bwa mem v0.7.17 | |
| # base-quality-recalibration: gatk4 v4.3.0.0 | |
| # realignment: none | |
| # variant-detection: strelka2 v2.9.10 | |
| # genotyping: none | |
| # reads: 200M | |
| # subcategory: NA12878-agilent | |
| # zenodo: | |
| # deposition: 7376244 | |
| # filename: WES_agilent_high_cov_sarek311_NA12878_strelka.vcf.gz | |
| # benchmark: giab-NA12878-agilent-200M | |
| # rename-contigs: resources/rename-contigs/ucsc-to-ensemb | |
| # TB-sarek311-deepvariants-agilent-75M: | |
| # labels: | |
| # site: TB QBiC | |
| # pipeline: nf-core/sarek v3.1.1 | |
| # trimming: Fastp v0.23.2 | |
| # read-mapping: bwa mem v0.7.17 | |
| # base-quality-recalibration: gatk4 v4.3.0.0 | |
| # realignment: none | |
| # variant-detection: DeepVariant v1.3.6 | |
| # genotyping: none | |
| # reads: 75M | |
| # subcategory: NA12878-agilent | |
| # zenodo: | |
| # deposition: 7376244 | |
| # filename: WES_agilent_low_cov_sarek311_NA12878_freebayes.vcf.gz | |
| # benchmark: giab-NA12878-agilent-75M | |
| # rename-contigs: resources/rename-contigs/ucsc-to-ensemb | |
| # TB-sarek311-freebayes-agilent-75M: | |
| # labels: | |
| # site: TB QBiC | |
| # pipeline: nf-core/sarek v3.1.1 | |
| # trimming: Fastp v0.23.2 | |
| # read-mapping: bwa mem v0.7.17 | |
| # base-quality-recalibration: gatk4 v4.3.0.0 | |
| # realignment: none | |
| # variant-detection: freebayes v1.3.6 | |
| # genotyping: none | |
| # reads: 75M | |
| # subcategory: NA12878-agilent | |
| # zenodo: | |
| # deposition: 7376244 | |
| # filename: WES_agilent_low_cov_sarek311_NA12878_freebayes.vcf.gz | |
| # benchmark: giab-NA12878-agilent-75M | |
| # rename-contigs: resources/rename-contigs/ucsc-to-ensemb | |
| # nfcore-sarek-${{ github.sha }}-haplotypecaller-agilent-75M: | |
| # labels: | |
| # site: nf-core | |
| # pipeline: nf-core/sarek v | |
| # trimming: Fastp v0.23.2 | |
| # read-mapping: bwa mem v0.7.17 | |
| # base-quality-recalibration: gatk4 v4.3.0.0 | |
| # realignment: none | |
| # variant-detection: gatk-haplotypecaller v4.3.0.0 | |
| # genotyping: none | |
| # reads: 75M | |
| # subcategory: NA12878-agilent | |
| # zenodo: | |
| # deposition: | |
| # filename: WES_agilent_low_cov_sarek311_NA12878_haplotypecaller.vcf.gz | |
| # benchmark: giab-NA12878-agilent-75M | |
| # rename-contigs: resources/rename-contigs/ucsc-to-ensemb | |
| # TB-sarek311-strelka-agilent-75M: | |
| # labels: | |
| # site: TB QBiC | |
| # pipeline: nf-core/sarek v3.1.1 | |
| # trimming: Fastp v0.23.2 | |
| # read-mapping: bwa mem v0.7.17 | |
| # base-quality-recalibration: gatk4 v4.3.0.0 | |
| # realignment: none | |
| # variant-detection: strelka2 v2.9.10 | |
| # genotyping: none | |
| # reads: 75M | |
| # subcategory: NA12878-agilent | |
| # zenodo: | |
| # deposition: 7376244 | |
| # filename: WES_agilent_low_cov_sarek311_NA12878_strelka.vcf.gz | |
| # benchmark: giab-NA12878-agilent-75M | |
| # rename-contigs: resources/rename-contigs/ucsc-to-ensemb |