From b81a1d5d5c3d1a15bdb0f1b25973f506868ddf12 Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Thu, 20 Jul 2023 11:29:09 +0100
Subject: [PATCH] fix preload

---
 .github/workflows/ancestry.yml          | 11 +++++++----
 .github/workflows/preload-reference.yml | 23 +++++++++++++----------
 2 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/ancestry.yml b/.github/workflows/ancestry.yml
index 78af620b..ca44aa79 100644
--- 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
index 48b642d9..4c041d8a 100644
--- a/.github/workflows/preload-reference.yml
+++ b/.github/workflows/preload-reference.yml
@@ -5,24 +5,19 @@ 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
@@ -30,3 +25,11 @@ jobs:
             ${{ 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
+