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Pipeline create - apply file permissions to new files #944

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Merged
ewels merged 5 commits into from
Mar 23, 2021
Merged

Pipeline create - apply file permissions to new files #944

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e6ccc10
Pipeline create - apply file permissions to new files
ewels Mar 23, 2021
2013dd1
File perms on nf-core modules create too
ewels Mar 23, 2021
dcec829
Changelog
ewels Mar 23, 2021
b28dcaf
Sometimes I ❤️ CI tests
ewels Mar 23, 2021
618179c
Update CHANGELOG.md
ewels Mar 23, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -4,6 +4,7 @@

* Added better logging message if a user doesn't specificy the directory correctly with `nf-core modules` commands [[#942](https://github.com/nf-core/tools/pull/942)]
* Fixed parameter validation bug caused by JSONObject [[#937](https://github.com/nf-core/tools/issues/937)]
* Fixed template creation error regarding file permissions [[#932](https://github.com/nf-core/tools/issues/932)]
* Split the `create-lint-wf` tests up into separate steps in GitHub Actions to make the CI results easier to read
* Added automated PR comments to the Markdownlint and Python Black lint CI tests to explain failures

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4 changes: 4 additions & 0 deletions nf_core/create.py
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Expand Up @@ -134,6 +134,10 @@ def render_template(self):
shutil.copy(template_fn_path, output_path)
continue

# Mirror file permissions
template_stat = os.stat(template_fn_path)
os.chmod(output_path, template_stat.st_mode)

# Make a logo and save it
self.make_pipeline_logo()

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4 changes: 4 additions & 0 deletions nf_core/modules/create.py
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Expand Up @@ -236,6 +236,10 @@ def render_template(self):
log.debug(f"Writing output to: '{dest_fn}'")
fh.write(rendered_output)

# Mirror file permissions
template_stat = os.stat(os.path.join("nf_core", "module-template", template_fn))
os.chmod(dest_fn, template_stat.st_mode)

def get_repo_type(self, directory):
"""
Determine whether this is a pipeline repository or a clone of
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