From 01552c7577606988642968ea5fc00613dd219be1 Mon Sep 17 00:00:00 2001
From: Matthias Zepper <MatthiasZepper@users.noreply.github.com>
Date: Thu, 26 Sep 2024 12:09:21 +0200
Subject: [PATCH] Add raw statements for template and update Singularity
 version in runner.

---
 .../.github/workflows/download_pipeline.yml     | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 03a906536..a5072850f 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -39,9 +39,11 @@ jobs:
         with:
           python-version: "3.12"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.4
 
       - name: Install dependencies
         run: |
@@ -77,7 +79,7 @@ jobs:
       - name: Count the downloaded number of container images
         id: count_initial
         run: |
-          image_count=$(ls -1 ./singularity_container_images | wc -l)
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Initial container image count: $image_count"
           echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
 
@@ -99,15 +101,18 @@ jobs:
       - name: Count the downloaded number of container images
         id: count_afterwards
         run: |
-          image_count=$(ls -1 ./singularity_container_images | wc -l)
-          echo "Post-pipeline container image count: $image_count"
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Post-pipeline run container image count: $image_count"
           echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
 
       - name: Compare container image counts
         run: |
+          {% raw %}
           if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
-            echo "The number of container images has changed. The pipeline has no support for offline runs!"
+            echo "$(expr ${{ env.IMAGE_COUNT_AFTER }}-${{ env.IMAGE_COUNT_INITIAL }}) additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
+            tree ./singularity_container_images
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"
           fi
+          {% endraw %}