nf-core download: Fix forgotten symlinks in cache.

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -69,7 +69,7 @@ jobs:
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 

nf_core/pipelines/download.py

@@ -1354,9 +1354,10 @@ def singularity_download_image(
                 log.debug(f"Copying {container} from cache: '{os.path.basename(out_path)}'")
                 progress.update(task, description="Copying from cache to target directory")
                 shutil.copyfile(cache_path, out_path)
+                self.symlink_singularity_images(cache_path)  # symlinks inside the cache directory
 
             # Create symlinks to ensure that the images are found even with different registries being used.
-            self.symlink_singularity_images(output_path)
+            self.symlink_singularity_images(out_path)
 
             progress.remove_task(task)
 
@@ -1465,9 +1466,10 @@ def singularity_pull_image(
             log.debug(f"Copying {container} from cache: '{os.path.basename(out_path)}'")
             progress.update(task, current_log="Copying from cache to target directory")
             shutil.copyfile(cache_path, out_path)
+            self.symlink_singularity_images(cache_path)  # symlinks inside the cache directory
 
         # Create symlinks to ensure that the images are found even with different registries being used.
-        self.symlink_singularity_images(output_path)
+        self.symlink_singularity_images(out_path)
 
         progress.remove_task(task)