fix preload

PGScatalog · Jul 20, 2023 · b81a1d5 · b81a1d5
1 parent baf1325
commit b81a1d5
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Showing 2 changed files with 20 additions and 14 deletions.
diff --git a/.github/workflows/ancestry.yml b/.github/workflows/ancestry.yml
@@ -17,15 +17,18 @@ on:
 env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/singularity
   SINGULARITY_VERSION: 3.8.3
-  ANCESTRY_REF_DIR: ${{ env.runner_temp }}
-  ANCESTRY_TARGET_DIR: ${{ env.runner_temp }}
 
 jobs:
   docker:
     if: ${{ inputs.docker }}
     runs-on: ubuntu-latest
 
-    steps:      
+    steps:
+      - name: Set environment variables
+        run: |
+          echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
+          echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
+      
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
@@ -37,7 +40,7 @@ jobs:
         uses: actions/cache/restore@v3
         with:
           path: ${{ runner.temp }}/docker
-          key: ${{ inputs.cache-key }}
+          key: ${{ inputs.container-cache-key }}
           fail-on-cache-miss: true
 
       - name: Load docker images from cache

diff --git a/.github/workflows/preload-reference.yml b/.github/workflows/preload-reference.yml
@@ -5,28 +5,31 @@ on:
     outputs:
       cache-key:
         value: ancestry
-
-env:
-  ANCESTRY_REF_DIR: ${{ env.RUNNER_TEMP }}
-  ANCESTRY_TARGET_DIR: ${{ env.RUNNER_TEMP }}  
 
 jobs:
   preload_reference:
     runs-on: ubuntu-latest
     steps:
-      - name: Download reference data
+      - name: Set environment variables
         run: |
-          wget -qnc -P $ANCESTRY_REF_DIR https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/GRCh38_HAPNEST_reference.tar.zst
-          wget -qnc -P $ANCESTRY_TARGET_DIR https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/GRCh38_HAPNEST_target.tar.zst
-          tar -xf $ANCESTRY_TARGET_DIR/GRCh38_HAPNEST_target.tar.zst -C $ANCESTRY_TARGET_DIR
-          
+          echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
+          echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
+
       - name: Cache reference data
         id: cache-ref
-        uses: actions/cache/save@v3
+        uses: actions/cache@v3
         with:
           path: |
             ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen
             ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.psam
             ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pvar.zst
             ${{ env.ANCESTRY_REF_DIR }}/GRCh38_HAPNEST_reference.tar.zst
           key: ancestry
+
+      - name: Download reference data
+        if: steps.cache-ref.outputs.cache-hit != 'true'        
+        run: |
+          wget -qnc -P $ANCESTRY_REF_DIR https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/GRCh38_HAPNEST_reference.tar.zst
+          wget -qnc -P $ANCESTRY_TARGET_DIR https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/GRCh38_HAPNEST_target.tar.zst
+          tar -xf $ANCESTRY_TARGET_DIR/GRCh38_HAPNEST_target.tar.zst -C $ANCESTRY_TARGET_DIR
+