Add info message with suggestion how to add the explicit library to t…

…he registries to test.

CHANGELOG.md

@@ -13,6 +13,7 @@
 ### Download
 
 - Improved container image resolution and prioritization of http downloads over Docker URIs ([#2364](https://github.com/nf-core/tools/pull/2364)).
+- Explicit container registry specifications will be ignored, so registries provided with `-l`/`--container-library` are used instead. ([#2403](https://github.com/nf-core/tools/pull/2403)).
 
 ### Linting
 
@@ -36,9 +37,9 @@
 - `params.max_multiqc_email_size` is no longer required ([#2273](https://github.com/nf-core/tools/pull/2273))
 - Remove `cleanup = true` from `test_full.config` in pipeline template ([#2279](https://github.com/nf-core/tools/pull/2279))
 - Fix usage docs for specifying `params.yaml` ([#2279](https://github.com/nf-core/tools/pull/2279))
-- Added stub in modules template ([#2277])(https://github.com/nf-core/tools/pull/2277) [Contributed by @nvnieuwk]
-- 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)
+- Added stub in modules template ([#2277])(<https://github.com/nf-core/tools/pull/2277>) [Contributed by @nvnieuwk]
+- 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))
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
 - Updates seqeralabs/action-tower-launch to v2.0.0 ([#2301](https://github.com/nf-core/tools/pull/2301))
@@ -79,7 +80,7 @@ _In addition, `-r` / `--revision` has been changed to a parameter that can be pr
 ### Linting
 
 - Warn if container access is denied ([#2270](https://github.com/nf-core/tools/pull/2270))
-- Error if module container specification has quay.io as prefix when it shouldn't have ([#2278])(https://github.com/nf-core/tools/pull/2278/files)
+- Error if module container specification has quay.io as prefix when it shouldn't have ([#2278])(<https://github.com/nf-core/tools/pull/2278/files>)
 - Detect if container is 'simple name' and try to contact quay.io server by default ([#2281](https://github.com/nf-core/tools/pull/2281))
 - Warn about null/None/empty default values in `nextflow_schema.json` ([#3328](https://github.com/nf-core/tools/pull/2328))
 - Fix linting when creating a pipeline skipping some parts of the template and add CI test ([#2330](https://github.com/nf-core/tools/pull/2330))
@@ -110,7 +111,7 @@ _In addition, `-r` / `--revision` has been changed to a parameter that can be pr
 - Consistent syntax for branch checks in PRs ([#2202](https://github.com/nf-core/tools/issues/2202))
 - Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
 - Updated AWS tests to use newly moved `seqeralabs/action-tower-launch` instead of `nf-core/tower-action`
-- Remove `.cff` files from `.editorconfig` [(#2145)[https://github.com/nf-core/tools/pull/2145]]
+- Remove `.cff` files from `.editorconfig` [[#2145](https://github.com/nf-core/tools/pull/2145)]
 - Simplify pipeline README ([#2186](https://github.com/nf-core/tools/issues/2186))
 - Added support for the apptainer container engine via `-profile apptainer`. ([#2244](https://github.com/nf-core/tools/issues/2244)) [Contributed by @jfy133]
 - Added config `docker.registry` to pipeline template for a configurable default container registry when using Docker containers. Defaults to `quay.io` ([#2133](https://github.com/nf-core/tools/pull/2133))
@@ -1137,7 +1138,7 @@ making a pull-request. See [`.github/CONTRIBUTING.md`](.github/CONTRIBUTING.md)
 - Move `params`section from `base.config` to `nextflow.config`
 - Use `env` scope to export `PYTHONNOUSERSITE` in `nextflow.config` to prevent conflicts with host Python environment
 - Bump minimum Nextflow version to `19.10.0` - required to properly use `env` scope in `nextflow.config`
-- Added support for nf-tower in the travis tests, using public mailbox nf-core@mailinator.com
+- Added support for nf-tower in the travis tests, using public mailbox <nf-core@mailinator.com>
 - Add link to [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and [Semantic Versioning](http://semver.org/spec/v2.0.0.html) to CHANGELOG
 - Adjusted `.travis.yml` checks to allow for `patch` branches to be tested
 - Add Python 3.7 dependency to the `environment.yml` file

nf_core/download.py

@@ -1238,9 +1238,15 @@ def singularity_pull_image(self, container, out_path, cache_path, library, progr
 
         # Sometimes, container still contain an explicit library specification, which
         # results in attempted pulls e.g. from docker://quay.io/quay.io/qiime2/core:2022.11
+        # Thus, we trim whatever precedes the base image specification, but also
+        # issue a warning about that behavior.
         container_parts = container.split("/")
         if len(container_parts) > 2:
             container = "/".join(container_parts[-2:])
+            found_library = container_parts[-3]
+            log.info(
+                f'Found explicit container library [bright_magenta]{found_library}[/] in a module. Upon pull failure, retry the download with [bright_magenta] -l "{found_library}"[/]'
+            )
 
         # Pull using singularity
         address = f"docker://{library}/{container.replace('docker://', '')}"