diff --git a/CHANGELOG.md b/CHANGELOG.md
index fde3775e70..89d3fe8f8f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@
 - Move registry definitions out of profile scope ([#2286])(https://github.com/nf-core/tools/pull/2286)
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
+
 ### Download
 
 - Introduce a `--tower` flag for `nf-core download` to obtain pipelines in an offline format suited for [seqeralabs® Nextflow Tower](https://cloud.tower.nf/) ([#2247](https://github.com/nf-core/tools/pull/2247)).
diff --git a/nf_core/download.py b/nf_core/download.py
index 5d214d2aaf..274132f02b 100644
--- a/nf_core/download.py
+++ b/nf_core/download.py
@@ -108,10 +108,10 @@ def __init__(
         self.force = force
         self.tower = tower
         self.include_configs = None
-        self.container = container if not singularity_cache_index else "singularity"
-        self.singularity_cache = (
-            singularity_cache if not singularity_cache_index else "remote"
-        )  # if a singularity_cache_index is given, use the file and overrule choice.
+        # force download of containers if a cache index is given or download is meant to be used for Tower.
+        self.container = "singularity" if singularity_cache_index or bool(tower) else container
+        # if a singularity_cache_index is given, use the file and overrule choice.
+        self.singularity_cache = "remote" if singularity_cache_index else singularity_cache
         self.singularity_cache_index = singularity_cache_index
         self.parallel_downloads = parallel_downloads
 
@@ -377,7 +377,7 @@ def prompt_config_inclusion(self):
     def prompt_container_download(self):
         """Prompt whether to download container images or not"""
 
-        if self.container is None and stderr.is_interactive:
+        if self.container is None and stderr.is_interactive and not self.tower:
             stderr.print("\nIn addition to the pipeline code, this tool can download software containers.")
             self.container = questionary.select(
                 "Download software container images:",
@@ -722,7 +722,7 @@ def find_container_images(self, workflow_directory):
                                 Therefore, we need to repeat the search over the contents, extract the variable name, and use it inside a new regex.
 
                                 To get the variable name ( ${container_id} in above example ), we match the literal word "container" and use lookbehind (reset the match).
-                                Then we skip [^\${}]+ everything that is not $ or curly braces. The next capture group is
+                                Then we skip [^${}]+ everything that is not $ or curly braces. The next capture group is
                                 ${ followed by any characters that are not curly braces [^{}]+ and ended by a closing curly brace (}),
                                 but only if it's not followed by any other curly braces (?![^{]*}). The latter ensures we capture the innermost
                                 variable name.
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 8150e7e839..31b8adca3a 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -283,7 +283,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
                 docker_tag = NoneD
             if l.startswith("quay.io/"):
-                l_stripped = re.sub("\W+$", "", l)
+                l_stripped = re.sub(r"\W+$", "", l)
                 self.failed.append(
                     (
                         "container_links",
diff --git a/tests/test_download.py b/tests/test_download.py
index 41fb9c625f..aa2e959f3d 100644
--- a/tests/test_download.py
+++ b/tests/test_download.py
@@ -190,7 +190,7 @@ def test_remote_container_functionality(self, tmp_dir):
 
         download_obj.include_configs = False  # suppress prompt, because stderr.is_interactive doesn't.
 
-        # test if settings are changed accordingly.
+        # test if the settings are changed to mandatory defaults, if an external cache index is used.
         assert download_obj.singularity_cache == "remote" and download_obj.container == "singularity"
         assert isinstance(download_obj.containers_remote, list) and len(download_obj.containers_remote) == 0
         # read in the file
@@ -264,9 +264,11 @@ def test_download_workflow_for_tower(self, tmp_dir):
         # corroborate that the other revisions are inaccessible to the user.
         assert len(download_obj.workflow_repo.tags) == len(download_obj.revision)
 
-        # manually test container image detection for 3.7 revision
+        # download_obj.download_workflow_tower(location=tmp_dir) will run container image detection for all requested revisions
+        assert isinstance(download_obj.containers, list) and len(download_obj.containers) == 33
+        # manually test container image detection for 3.7 revision only
+        download_obj.containers = []  # empty container list for the test
         download_obj.workflow_repo.checkout(download_obj.wf_sha["3.7"])
-        assert isinstance(download_obj.containers, list) and len(download_obj.containers) == 0
         download_obj.find_container_images(download_obj.workflow_repo.access())
         assert len(download_obj.containers) == 30  # 30 containers for 3.7
         assert (