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Catch AssertionError from schema build #1267

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merged 4 commits into from
Nov 16, 2021
Merged

Catch AssertionError from schema build #1267

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462cb65
Catch AssertionError from schema build
ewels Sep 7, 2021
da5b057
Merge branch 'master' into ewels-patch-1
ewels Sep 7, 2021
9fc8cdd
Merge branch 'master' into ewels-patch-1
ewels Nov 16, 2021
a135b8e
Print stdout as well as stderr on nextflow command errors.
ewels Nov 16, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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2 changes: 1 addition & 1 deletion nf_core/__main__.py
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Expand Up @@ -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)

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2 changes: 1 addition & 1 deletion nf_core/utils.py
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Expand Up @@ -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()}"
)


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