diff --git a/.github/workflows/ncbench.yml b/.github/workflows/ncbench.yml index 614e2dd722..30d9eaaa13 100644 --- a/.github/workflows/ncbench.yml +++ b/.github/workflows/ncbench.yml @@ -4,11 +4,11 @@ name: NCBench Zenodo Upload on: # upload can only be triggered manually for now workflow_dispatch: - inputs: - germline_wes: - description: "Trigger NCBench upload" - type: boolean - default: true + inputs: + germline_wes: + description: "Trigger NCBench upload" + type: boolean + default: true pull_request: jobs: @@ -28,206 +28,8 @@ jobs: uses: keithweaver/aws-s3-github-action@v1.0.0 if: ${{ matrix.enabled }} with: - revision: ${{ github.sha }} - source: s3://nf-core-awsmegatests/sarek/results-test-59026dc07633edb83aab3bfb2f65f79db38437a1/test_full/variant_calling/strelka/ + source: s3://nf-core-awsmegatests/sarek/results-test-59026dc07633edb83aab3bfb2f65f79db38437a1/test_full/variant_calling/strelka command: sync + aws_region: eu-west-1 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 github-actions@github.com -# 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