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@ewels ewels commented Mar 15, 2021

Port the pipeline template to use Jinja2 directly instead of cookiecutter, following on from this process for the module template in #878

Makes for cleaner code, nicer file structures (no more file paths with annoying curly braces) and one fewer dependencies.

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codecov bot commented Mar 16, 2021

Codecov Report

Merging #880 (f6e0cf5) into dev (fa17a9e) will increase coverage by 0.12%.
The diff coverage is 92.30%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #880      +/-   ##
==========================================
+ Coverage   70.52%   70.65%   +0.12%     
==========================================
  Files          33       33              
  Lines        3651     3673      +22     
==========================================
+ Hits         2575     2595      +20     
- Misses       1076     1078       +2     
Impacted Files Coverage Δ
nf_core/sync.py 51.83% <ø> (ø)
nf_core/__main__.py 61.33% <66.66%> (ø)
nf_core/lint/template_strings.py 85.00% <75.00%> (ø)
nf_core/create.py 93.68% <94.23%> (-0.77%) ⬇️
nf_core/lint/__init__.py 79.72% <100.00%> (ø)
nf_core/modules/create.py 63.57% <100.00%> (ø)
nf_core/schema.py 86.51% <100.00%> (-0.04%) ⬇️

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@ewels ewels added ready-for-review template nf-core pipeline/component template labels Mar 16, 2021
@maxulysse
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Love the idea

@KevinMenden
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Okay everything worked fine for me. Run the same commands with this and the old cookiecutter tool.

  • All module files are identical
  • Did not catch any differences in pipelines created from the template
  • --force works for overwriting a module

Will look a bit deeper to be even more on the safe side but so far everything looks good! 👍

@ewels ewels merged commit a44bf6c into nf-core:dev Mar 16, 2021
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ewels commented Mar 16, 2021

Approved on Slack ✅

@ewels ewels deleted the pipeline-jinja branch March 16, 2021 09:46
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4 participants