Handle CI for demux step with singularity

WEHIGenomicsRnD · Feb 26, 2024 · 7d8d919 · 7d8d919
1 parent 1ea7c9a
commit 7d8d919
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -31,6 +31,9 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Install Singularity
+        uses: singularityhub/install-singularity@main
+
       - name: Run pipeline with test data
         run: |
           cd ${GITHUB_WORKSPACE}

diff --git a/nextflow.config b/nextflow.config
@@ -15,7 +15,7 @@ params {
 
     index_template_file     = "$projectDir/.test/data/indexes.txt"
 
-    demultiplex             = false
+    demultiplex             = true
 
     //number of bases to search for index 1 at start of read
     bases_num_r1            = 12
@@ -70,6 +70,7 @@ profiles {
     }
     test {
         conda.enabled = true
+        singularity.enabled = true
         stubRun = true
         cleanup = false
         process.memory = '1 GB'