From bdc1cd97bdbd59d3e94a76f789de46955ad90237 Mon Sep 17 00:00:00 2001
From: Zohaib Anwar <zohaib_anwar@ymail.com>
Date: Sun, 15 Dec 2024 23:50:47 -0800
Subject: [PATCH] update workflow singularity

---
 .github/workflows/nextflow_CI.yml | 38 ++++++++++++++++++++++++++++---
 1 file changed, 35 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/nextflow_CI.yml b/.github/workflows/nextflow_CI.yml
index 310f7e9..b54410e 100644
--- 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