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only check pipeline name without dashes if the name is provided by prompt #2123

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Merged
ewels merged 5 commits into from
Dec 13, 2022
+9 −5
Merged

only check pipeline name without dashes if the name is provided by prompt #2123

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2b96d32
Merge branch 'dev' of https://github.com/nf-core/tools into dev
mirpedrol Dec 12, 2022
6a7da79
only check pipeline name without dashes if the name is provided by pr…
mirpedrol Dec 12, 2022
ffc3bd3
Merge branch 'dev' of https://github.com/nf-core/tools into dev
mirpedrol Dec 12, 2022
d97e116
Merge branch 'dev' of https://github.com/mirpedrol/tools into dashed-…
mirpedrol Dec 12, 2022
5ccbae8
update changelog
mirpedrol Dec 12, 2022
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,8 @@

### General

- Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))

## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]

- Patch release to fix pipeline sync ([#2110](https://github.com/nf-core/tools/pull/2110))
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7 changes: 4 additions & 3 deletions nf_core/create.py
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Expand Up @@ -173,9 +173,10 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
and "manifest.name" in config_yml["lint"]["nextflow_config"]
):
return param_dict, skip_paths
# Check that the pipeline name matches the requirements
if not re.match(r"^[a-z]+$", param_dict["short_name"]):
raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
if param_dict["prefix"] == "nf-core":
# Check that the pipeline name matches the requirements
if not re.match(r"^[a-z]+$", param_dict["short_name"]):
raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")

return param_dict, skip_paths

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5 changes: 3 additions & 2 deletions nf_core/sync.py
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Expand Up @@ -252,8 +252,9 @@ def make_template_pipeline(self):
plain=True,
).init_pipeline()
except Exception as err:
# If sync fails, remove template_yaml_path before raising error.
os.remove(self.template_yaml_path)
if self.template_yaml_path:
# If sync fails, remove template_yaml_path before raising error.
os.remove(self.template_yaml_path)
# Reset to where you were to prevent git getting messed up.
self.repo.git.reset("--hard")
raise SyncException(f"Failed to rebuild pipeline from template with error:\n{err}")
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