Add fail-warned to pipeline linting workflow

[mirpedrol]

The GitHub workflow for pipeline linting does not fail on warnings.

• Add --fail-warned option to nf-core lint to make the warnings fail.
• Remove TODO statements from template pipeline in the linting workflow. Those lines are expected to produce a warning during linting.
• Add --fail-warned to pipeline linting workflow

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 #1593 (dd6d0a1) into dev (34d472f) will increase coverage by 0.08%.
The diff coverage is 81.81%.

@@            Coverage Diff             @@
##              dev    #1593      +/-   ##
==========================================
+ Coverage   64.63%   64.71%   +0.08%     
==========================================
  Files          54       54              
  Lines        6249     6235      -14     
==========================================
- Hits         4039     4035       -4     
+ Misses       2210     2200      -10     

Impacted Files	Coverage Δ
nf_core/__main__.py	50.66% <66.66%> (+0.11%)	⬆️
nf_core/lint/__init__.py	74.59% <87.50%> (+1.20%)	⬆️
nf_core/lint/files_unchanged.py	73.33% <0.00%> (-2.67%)	⬇️
nf_core/lint_utils.py	86.66% <0.00%> (-0.44%)	⬇️
nf_core/modules/bump_versions.py	64.60% <0.00%> (-0.23%)	⬇️
nf_core/sync.py	52.23% <0.00%> (-0.22%)	⬇️
nf_core/modules/lint/__init__.py	82.52% <0.00%> (-0.19%)	⬇️
nf_core/list.py	79.91% <0.00%> (ø)
nf_core/create.py	85.93% <0.00%> (ø)
nf_core/schema.py	77.24% <0.00%> (ø)
... and 36 more

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[ggabernet]

Looks good to me!