diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index b0464d2741..2a50663971 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -89,7 +89,7 @@ jobs:
 
       - name: Set Git default branch from nextflow.config and set git default branch to that or "master"
         run: |
-          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
+          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nf-core/${{ matrix.pipeline }}/nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
           if [ -z "$defaultBranch" ]; then
             defaultBranch="master"
           fi