From b1a31c8c078e516a5dff6afa9d26962a961ca991 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Sat, 15 Jun 2024 14:34:30 +0200
Subject: [PATCH] Update nf-test version

---
 .github/workflows/ci-tests.yml | 45 ++++++++++++++++++++--------------
 1 file changed, 27 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 617cc94..e15aa41 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -7,23 +7,32 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        shard: [1, 2, 3]
+
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up JDK 11
-      uses: actions/setup-java@v2
-      with:
-        java-version: '11'
-        distribution: 'adopt'
-    - name: Install nextflow
-      run: sudo bash; mkdir /opt/nextflow; cd /opt/nextflow; wget https://github.com/nextflow-io/nextflow/releases/download/v21.04.3/nextflow; chmod +x nextflow;
-    - name: Add nextflow to path
-      run: echo "/opt/nextflow" >> $GITHUB_PATH;
-    - name: Install nf-test
-      run: sudo bash; mkdir /opt/nf-test; cd /opt/nf-test; wget https://github.com/askimed/nf-test/releases/download/v0.8.0-rc1/nf-test-0.8.0-rc1.tar.gz; tar xvfz nf-test-*.tar.gz; chmod +x nf-test;
-    - name: Add nf-test to path
-      run: echo "/opt/nf-test" >> $GITHUB_PATH;
-    - name: Build Docker 
-      run:  docker build -t genepi/imputation-docker .     
-    - name: Run Tests 
-      run:  nf-test test
+      - uses: actions/checkout@v2
+      
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+          
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "latest-edge"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- get.nf-test.com | bash  -s 0.9.0-rc2
+          sudo mv nf-test /usr/local/bin/
+          
+      - name: Build Docker 
+        run:  docker build -t genepi/imputation-docker .
+        
+      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
+        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }}