run_analysis.yml

name: CI

on:
  pull_request:
  workflow_dispatch:

jobs:
  build_and_publish_image:
    name: Build and Publish Image
    runs-on: ubuntu-latest-m
    steps:
      - uses: actions/checkout@v3
        with:
          token: ${{ secrets.GH_TOKEN }}
      - uses: dorny/paths-filter@v2
        id: changes
        with:
          filters: |
            dockerfile:
              - 'Dockerfile'

      - name: Set up Docker Buildx
        if: steps.changes.outputs.dockerfile == 'true'
        uses: docker/setup-buildx-action@v2

      - name: Docker meta
        if: steps.changes.outputs.dockerfile == 'true'
        id: meta
        uses: docker/metadata-action@v4
        with:
          images: pgc-images.sbgenomics.com/d3b-bixu/open-pedcan
          tags: |
            type=raw,value=analysisjob

      - name: Login to DockerHub
        if: steps.changes.outputs.dockerfile == 'true'
        uses: docker/login-action@v2
        with:
          registry: pgc-images.sbgenomics.com
          username: ${{ secrets.DOCKER_HUB_USERNAME }}
          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

      - name: Build and push
        if: steps.changes.outputs.dockerfile == 'true'
        uses: docker/build-push-action@v3
        with:
          context: .
          push: true
          tags: ${{ steps.meta.outputs.tags }}
          cache-from: type=gha
          cache-to: type=gha,mode=max
          build-args: github_pat=${{ secrets.GITHUB_TOKEN }}

  run_analysis:
    name: Run Analysis
    needs: build_and_publish_image
    runs-on: ubuntu-latest
    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 - 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
            
          - name: Molecular Subtyping - ATRT
            entrypoint: molecular-subtyping-ATRT/run-molecular-subtyping-ATRT.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: 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: 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@v3
      - uses: dorny/paths-filter@v2
        id: changes
        with:
          filters: |
            dockerfile:
              - 'Dockerfile'

      - name: Set image tag to analysisjob
        if: steps.changes.outputs.dockerfile == 'true'
        run: |
         echo "DOCKER_IMAGE_NAME=pgc-images.sbgenomics.com/d3b-bixu/open-pedcan:analysisjob" >> $GITHUB_ENV
  
      - name: Set image tag to latest
        if: steps.changes.outputs.dockerfile != 'true'
        run: |
         echo "DOCKER_IMAGE_NAME=pgc-images.sbgenomics.com/d3b-bixu/open-pedcan:latest" >> $GITHUB_ENV

      - name: Download Data 
        if: steps.changes.outputs.dockerfile != 'true'
        uses: "docker://${{env.DOCKER_IMAGE_NAME}}"
        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
        if: steps.changes.outputs.dockerfile == 'true'
        uses: "docker://${{env.DOCKER_IMAGE_NAME}}"
        with:
          entrypoint: analyses/${{ 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 }}