create separate yaml scripts for mem-intensive jobs

d3b-center · Dec 11, 2023 · 4d8aa58 · 4d8aa58
1 parent 4802aa0
commit 4d8aa58
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Showing 3 changed files with 78 additions and 33 deletions.
diff --git a/.github/workflows/run_analysis_cranio.yml b/.github/workflows/run_analysis_cranio.yml
@@ -0,0 +1,39 @@
+name: Analysis - CRANIO
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  run_analysis:
+    name: Run Analysis - Cranio
+    runs-on: large-runner-32
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # Molecular subtyping modules
+          - name: Molecular Subtyping - CRANIO
+            entrypoint: molecular-subtyping-CRANIO/run-molecular-subtyping-cranio.sh
+            openpbta_subset: 0
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Download Data
+        uses: docker://pgc-images.sbgenomics.com/d3b-bixu/open-pedcan: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/open-pedcan: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 }}
diff --git a/.github/workflows/run_analysis.yml → .github/workflows/run_analysis_parallel.yml b/.github/workflows/run_analysis.yml → .github/workflows/run_analysis_parallel.yml
@@ -1,12 +1,12 @@
-name: Analysis
+name: Analysis - Parallel
 
 on:
   pull_request:
   workflow_dispatch:
 
 jobs:
   run_analysis:
-    name: Run Analysis
+    name: Run Analysis - Parallel
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -17,17 +17,6 @@ jobs:
             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
@@ -40,10 +29,6 @@ jobs:
 
           - 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
@@ -70,30 +55,14 @@ jobs:
             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
 

diff --git a/.github/workflows/run_analysis_tp53.yml b/.github/workflows/run_analysis_tp53.yml
@@ -0,0 +1,37 @@
+name: Analysis - TP53
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  run_analysis:
+    name: Run Analysis - TP53
+    runs-on: large-runner-32
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: TP53/NF1 scores
+            entrypoint: tp53_nf1_score/run_classifier.sh
+            openpedcan_polya_strand: 0
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Download Data
+        uses: docker://pgc-images.sbgenomics.com/d3b-bixu/open-pedcan: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/open-pedcan: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 }}