Merge branch 'dev' into rm_nfcore_external_java_deps

Author: mashehu

CHANGELOG.md

@@ -11,6 +11,8 @@
 - Add conda channel order to nextflow.config ([#2094](https://github.com/nf-core/tools/pull/2094))
 - Fix tyop in pipeline nextflow.config ([#2664](https://github.com/nf-core/tools/pull/2664))
 - Remove `nfcore_external_java_deps.jar` from lib directory in pipeline template ([#2675](https://github.com/nf-core/tools/pull/2675))
+- Add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
+- Add new pipeline error message pointing to docs when 'requirement exceeds available memory' error message ([#2680](https://github.com/nf-core/tools/pull/2680))
 
 ### Download
 
@@ -39,6 +41,7 @@
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.13 ([#2660](https://github.com/nf-core/tools/pull/2660))
 - Add new subcommand: `nf-core logo-create` to output an nf-core logo for a pipeline (instead of going through the website) ([#2662](https://github.com/nf-core/tools/pull/2662))
 - Update actions/cache action to v4 ([#2666](https://github.com/nf-core/tools/pull/2666))
+- Handle api redirects from the old site ([#2672](https://github.com/nf-core/tools/pull/2672))
 - Remove redundanct v in pipeline version for emails ([#2667](https://github.com/nf-core/tools/pull/2667))
 - add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
 

nf_core/pipeline-template/workflows/pipeline.nf

@@ -127,6 +127,13 @@ workflow.onComplete {
     }
 }
 
+workflow.onError {
+    if (workflow.errorReport.contains("Process requirement exceeds available memory")) {
+        println("🛑 Default resources exceed availability 🛑 ")
+        println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡")
+    }
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END

nf_core/utils.py

@@ -420,11 +420,14 @@ def poll_nfcore_web_api(api_url, post_data=None):
         except requests.exceptions.ConnectionError:
             raise AssertionError(f"Could not connect to URL: {api_url}")
         else:
-            if response.status_code != 200:
+            if response.status_code != 200 and response.status_code != 301:
                 log.debug(f"Response content:\n{response.content}")
                 raise AssertionError(
                     f"Could not access remote API results: {api_url} (HTML {response.status_code} Error)"
                 )
+            # follow redirects
+            if response.status_code == 301:
+                return poll_nfcore_web_api(response.headers["Location"], post_data)
             try:
                 web_response = json.loads(response.content)
                 if "status" not in web_response: