Save pipeline template info to .nf-core.yml

[mirpedrol]

When customizing the pipeline template, information was saved to a file named pipeline_template.yml. This PR deprecates such file and stores the info to .nf-core.yml instead.

Partially close #2359 (needs a follow-up PR moving data from pipeline_tamplate.yml in old pipelines)

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

Merging #2388 (e8c289e) into dev (13f331e) will increase coverage by 0.01%.
Report is 6 commits behind head on dev.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##              dev    #2388      +/-   ##
==========================================
+ Coverage   71.05%   71.06%   +0.01%     
==========================================
  Files          87       87              
  Lines        9382     9384       +2     
==========================================
+ Hits         6666     6669       +3     
+ Misses       2716     2715       -1     

Files Changed	Coverage Δ
nf_core/lint/files_exist.py	78.00% <ø> (ø)
nf_core/create.py	83.03% <100.00%> (+0.12%)	⬆️

... and 1 file with indirect coverage changes