update MB SHH abridged output #655
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| name: Analysis | |
| on: | |
| pull_request: | |
| jobs: | |
| consensus_cn_manta: | |
| name: Run Analysis - Consensus CN Manta | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: free disk space | |
| run: | | |
| sudo swapoff -a | |
| sudo rm -f /swapfile | |
| sudo apt clean | |
| docker rmi $(docker image ls -aq) | |
| df -h | |
| - name: Download Data for Consensus CN Manta | |
| uses: docker://pgc-images.sbgenomics.com/d3b-bixu/openpedcanverse:latest | |
| with: | |
| entrypoint: ./download-data.sh | |
| env: | |
| OPENPEDCAN_URL: https://s3.amazonaws.com/d3b-openaccess-us-east-1-prd-pbta/open-targets | |
| OPENPEDCAN_RELEASE: testing | |
| - name: Run Consensus CN Manta | |
| uses: docker://pgc-images.sbgenomics.com/d3b-bixu/openpedcanverse:latest | |
| with: | |
| entrypoint: ./analyses/copy_number_consensus_call_manta/run_consensus_call.sh | |
| consensus_cn: | |
| name: Run Analysis - Consensus CN | |
| needs: consensus_cn_manta | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: free disk space | |
| run: | | |
| sudo swapoff -a | |
| sudo rm -f /swapfile | |
| sudo apt clean | |
| docker rmi $(docker image ls -aq) | |
| df -h | |
| - name: Download Data for Consensus CN | |
| uses: docker://pgc-images.sbgenomics.com/d3b-bixu/openpedcanverse:latest | |
| with: | |
| entrypoint: ./download-data.sh | |
| env: | |
| OPENPEDCAN_URL: https://s3.amazonaws.com/d3b-openaccess-us-east-1-prd-pbta/open-targets | |
| OPENPEDCAN_RELEASE: testing | |
| - name: Run Consensus CN | |
| uses: docker://pgc-images.sbgenomics.com/d3b-bixu/openpedcanverse:latest | |
| with: | |
| entrypoint: ./analyses/copy_number_consensus_call/run_consensus_call.sh | |
| run_analysis: | |
| name: Run Analysis | |
| runs-on: ubuntu-latest-m | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Molecular subtyping modules | |
| - name: Molecular Subtyping - MB | |
| entrypoint: molecular-subtyping-MB/run-molecular-subtyping-mb.sh | |
| openpbta_subset: 0 | |
| - name: Molecular Subtyping - CRANIO | |
| entrypoint: molecular-subtyping-CRANIO/run-molecular-subtyping-cranio.sh | |
| openpbta_subset: 0 | |
| - name: Molecular Subtyping - EPN | |
| entrypoint: molecular-subtyping-EPN/run-molecular-subtyping-EPN.sh | |
| - name: Molecular Subtyping - EMBRYONAL | |
| entrypoint: molecular-subtyping-embryonal/run-embryonal-subtyping.sh | |
| openpbta_testing: 1 | |
| - name: Molecular Subtyping - CHORDOMA | |
| entrypoint: molecular-subtyping-chordoma/run-molecular-subtyping-chordoma.sh | |
| openpbta_subset: 0 | |
| - name: Molecular Subtyping - EWS | |
| entrypoint: molecular-subtyping-EWS/run_subtyping.sh | |
| - name: Molecular Subtyping - NEUROCYTOMA | |
| entrypoint: molecular-subtyping-neurocytoma/run_subtyping.sh | |
| - name: Molecular Subtyping - HGG | |
| entrypoint: molecular-subtyping-HGG/run-molecular-subtyping-HGG.sh | |
| - name: Molecular Subtyping - LGG | |
| entrypoint: molecular-subtyping-LGAT/run_subtyping.sh | |
| openpbta_subset: 0 | |
| - name: Molecular Subtyping - ATRT | |
| entrypoint: molecular-subtyping-ATRT/run-molecular-subtyping-ATRT.sh | |
| - name: Molecular Subtyping - PB | |
| entrypoint: molecular-subtyping-PB/run-molecular-subtyping-PB.sh | |
| - name: Molecular Subtyping - NBL | |
| entrypoint: molecular-subtyping-NBL/run-molecular-subtyping-NBL.sh | |
| - name: Molecular Subtyping - PATHOLOGY/COMPILE | |
| entrypoint: molecular-subtyping-pathology/run-subtyping-aggregation.sh | |
| openpbta_testing: 1 | |
| - name: Molecular Subtyping - INTEGRATE (+ add cancer groups) | |
| entrypoint: molecular-subtyping-integrate/run-subtyping-integrate.sh | |
| # Analysis modules | |
| - name: Independent Specimens | |
| entrypoint: independent-samples/run-independent-samples.sh | |
| - name: Independent Specimens pre-release | |
| entrypoint: independent-samples/run-independent-samples.sh | |
| run_for_subtyping: 1 | |
| - name: Gene set enrichment | |
| entrypoint: gene-set-enrichment-analysis/run-gsea.sh | |
| run_for_subtyping: 1 | |
| openpbta_testing: 1 | |
| - name: TP53/NF1 scores | |
| entrypoint: tp53_nf1_score/run_classifier.sh | |
| openpedcan_polya_strand: 0 | |
| - name: Fusion filtering | |
| entrypoint: fusion_filtering/run_fusion_merged.sh | |
| - name: Fusion summary | |
| entrypoint: fusion-summary/run-new-analysis.sh | |
| openpbta_subset: 0 | |
| - name: Consensus CN Manta | |
| entrypoint: copy_number_consensus_call_manta/run_consensus_call.sh | |
| - name: Consensus CN | |
| entrypoint: copy_number_consensus_call/run_consensus_call.sh | |
| - name: Consensus CN annotation | |
| entrypoint: focal-cn-file-preparation/run-prepare-cn.sh | |
| openpbta_testing: 1 | |
| - name: TMB calculation | |
| entrypoint: tmb-calculation/run_tmb_calculation.sh | |
| - name: Mutational signatures | |
| entrypoint: mutational-signatures/run_mutational_signatures.sh | |
| openpbta_testing: 1 | |
| - name: Immune Deconvolution | |
| entrypoint: immune-deconv/run-immune-deconv.sh | |
| #- name: EFO/MONDO annotation | |
| # entrypoint: efo-mondo-mapping/run_search_and_qc.sh | |
| #- name: ENSEMBL Gene matching | |
| # entrypoint: gene_match/run-gene-mapping.sh | |
| #- name: Update table annotation data | |
| # entrypoint: long-format-table-utils/run-update-long-format-table-utils.sh | |
| #- name: RNA-Seq Expression Summary stats | |
| # entrypoint: rna-seq-expression-summary-stats/run-rna-seq-expression-summary-stats.sh | |
| # MTP-specific modules | |
| #- name: Fusion frequency tables | |
| # entrypoint: fusion-frequencies/run-frequencies.sh | |
| #- name: SNV frequency tables | |
| # entrypoint: snv-frequencies/run-snv-frequencies.sh | |
| #- name: CNV frequency tables | |
| # entrypoint: cnv-frequencies/run-cnv-frequencies-analysis.sh | |
| #- name: RNA-Seq batch correction | |
| # entrypoint: rnaseq-batch-correct/run_ruvseq.sh | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: free disk space | |
| run: | | |
| sudo swapoff -a | |
| sudo rm -f /swapfile | |
| sudo apt clean | |
| docker rmi $(docker image ls -aq) | |
| df -h | |
| - name: Download Data | |
| uses: docker://pgc-images.sbgenomics.com/d3b-bixu/openpedcanverse:latest | |
| with: | |
| entrypoint: ./download-data.sh | |
| env: | |
| OPENPEDCAN_URL: https://s3.amazonaws.com/d3b-openaccess-us-east-1-prd-pbta/open-targets | |
| OPENPEDCAN_RELEASE: testing | |
| - name: Run Analysis | |
| uses: docker://pgc-images.sbgenomics.com/d3b-bixu/openpedcanverse:latest | |
| with: | |
| entrypoint: analyses/${{ matrix.entrypoint }} | |
| env: | |
| OPENPBTA_SUBSET: ${{ matrix.openpbta_subset }} | |
| OPENPBTA_TESTING: ${{ matrix.openpbta_testing }} | |
| RUN_FOR_SUBTYPING: ${{ matrix.run_for_subtyping }} | |
| OPENPEDCAN_POLYA_STRAND: ${{ matrix.openpedcan_polya_strand }} | |