Download: Use '.partial' extensions whilst downloading.

To prevent accidentally using partial broken downloads, use an additional .partial file extension whilst download is running and rename the file to remove this when complete.

nf_core/download.py

@@ -478,7 +478,13 @@ def singularity_download_image(self, container, out_path, cache_path, progress):
         nice_name = container.split("/")[-1][:50]
         task = progress.add_task(nice_name, start=False, total=False, progress_type="download")
         try:
-            with open(output_path, "wb") as fh:
+            # Set a temporary filename to download to
+            output_path_tmp = f"{output_path}.partial"
+            if os.path.exists(output_path_tmp):
+                os.remove(output_path_tmp)
+
+            # Open file handle and download
+            with open(output_path_tmp, "wb") as fh:
                 # Disable caching as this breaks streamed downloads
                 with requests_cache.disabled():
                     r = requests.get(container, allow_redirects=True, stream=True, timeout=60 * 5)
@@ -492,13 +498,16 @@ def singularity_download_image(self, container, out_path, cache_path, progress):
                         progress.update(task, advance=len(data))
                         fh.write(data)
 
-                # Copy cached download if we are using the cache
-                if cache_path:
-                    log.debug("Copying {} from cache: '{}'".format(container, os.path.basename(out_path)))
-                    progress.update(task, description="Copying from cache to target directory")
-                    shutil.copyfile(cache_path, out_path)
+            # Rename partial filename to final filename
+            os.rename(output_path_tmp, output_path)
+
+            # Copy cached download if we are using the cache
+            if cache_path:
+                log.debug("Copying {} from cache: '{}'".format(container, os.path.basename(out_path)))
+                progress.update(task, description="Copying from cache to target directory")
+                shutil.copyfile(cache_path, out_path)
 
-                progress.remove_task(task)
+            progress.remove_task(task)
 
         except:
             # Kill the progress bars