test user override with env variable

Author: madscort

.github/workflows/nextflow-test-container.yml

@@ -28,17 +28,21 @@ jobs:
         key: docker-cache-${{ runner.os }}-${{ hashFiles('**/nextflow.config', '**/modules.config') }}
         restore-keys: |
           docker-cache-${{ runner.os }}-
-      
+
+    - name: Capture runner UID/GID
+      run: |
+          echo "UID=$(id -u)" >> $GITHUB_ENV
+          echo "GID=$(id -g)" >> $GITHUB_ENV
+
     - name: Install Nextflow
       run: |
         curl -s https://get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
         nextflow -version
 
-    - name: Ensure workspace writable
-      run: sudo chmod -R a+rwx "$GITHUB_WORKSPACE"
-
     - name: Run Nextflow pipeline with Docker
+      env:
+          NXF_DEFAULT_DOCKER_OPTS: "-u ${{ env.UID }}:${{ env.GID }}"
       run: |
         nextflow run main.nf -profile test -with-docker