update workflow singularity

cidgoh · Dec 16, 2024 · bdc1cd9 · bdc1cd9
1 parent dce1f37
commit bdc1cd9
Showing 1 changed file with 35 additions and 3 deletions.
diff --git a/.github/workflows/nextflow_CI.yml b/.github/workflows/nextflow_CI.yml
@@ -17,9 +17,25 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-      - name: Run pipeline test (default)
+      - name: Install Singularity
         run: |
-          nextflow run main.nf -profile docker --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml
+          sudo apt-get update && sudo apt-get install -y \
+            build-essential \
+            libssl-dev \
+            uuid-dev \
+            libgpgme11-dev \
+            squashfs-tools \
+            libseccomp-dev \
+            wget \
+            pkg-config \
+            git \
+            cryptsetup
+          wget https://github.com/sylabs/singularity/releases/download/v3.10.0/singularity-ce_3.10.0-focal_amd64.deb
+          sudo dpkg -i singularity-ce_3.10.0-focal_amd64.deb
+
+      - name: Run pipeline test (user)
+        run: |
+          nextflow run main.nf -profile singularity --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml
 
   test_sarscov2_reference:
     name: Run pipeline test (reference)
@@ -32,6 +48,22 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-      - name: Run pipeline test (alternative)
+      - name: Install Singularity
+        run: |
+          sudo apt-get update && sudo apt-get install -y \
+            build-essential \
+            libssl-dev \
+            uuid-dev \
+            libgpgme11-dev \
+            squashfs-tools \
+            libseccomp-dev \
+            wget \
+            pkg-config \
+            git \
+            cryptsetup
+          wget https://github.com/sylabs/singularity/releases/download/v3.10.0/singularity-ce_3.10.0-focal_amd64.deb
+          sudo dpkg -i singularity-ce_3.10.0-focal_amd64.deb
+
+      - name: Run pipeline test (reference)
         run: |
           nextflow run main.nf -profile singularity --prefix "covidmvp-$(date +%Y-%m-%d)" -params-file covidmvp_clinical_params.yaml