Pipeline jinja

[ewels]

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.

[codecov]

Codecov Report

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

@@            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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[maxulysse]

Love the idea

[KevinMenden]

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]

Approved on Slack ✅