Merge pull request #1267 from nf-core/ewels-patch-1

Catch AssertionError from schema build

CHANGELOG.md

@@ -20,6 +20,7 @@
 * Fixed bug in `nf-core list` when `NXF_HOME` is set
 * Run CI test used to create and lint/run the pipeline template with minimum and latest edge release of NF ([#1304](https://github.com/nf-core/tools/issues/1304))
 * New YAML issue templates for tools bug reports and feature requests, with a much richer interface ([#1165](https://github.com/nf-core/tools/pull/1165))
+* Handle synax errors in Nextflow config nicely when running `nf-core schema build` ([#1267](https://github.com/nf-core/tools/pull/1267))
 
 ### Modules
 

nf_core/__main__.py

@@ -668,7 +668,7 @@ def build(dir, no_prompts, web_only, url):
         schema_obj = nf_core.schema.PipelineSchema()
         if schema_obj.build_schema(dir, no_prompts, web_only, url) is False:
             sys.exit(1)
-    except UserWarning as e:
+    except (UserWarning, AssertionError) as e:
         log.error(e)
         sys.exit(1)
 

nf_core/utils.py

@@ -297,7 +297,7 @@ def nextflow_cmd(cmd):
             raise AssertionError("It looks like Nextflow is not installed. It is required for most nf-core functions.")
     except subprocess.CalledProcessError as e:
         raise AssertionError(
-            f"Command '{cmd}' returned non-zero error code '{e.returncode}':\n[red]> {e.stderr.decode()}"
+            f"Command '{cmd}' returned non-zero error code '{e.returncode}':\n[red]> {e.stderr.decode()}{e.stdout.decode()}"
         )