Refactor --hide-progress to be at the top level CLI

[ewels]

• Have --hide-progress shared at the top level of the CLI, instead of repeated for specific subcommands
  • nf-core --hide-progress lint instead of nf-core lint --hide-progress
  • Makes it easier to reuse in any subcommand
  • Remove slightly odd code to share common CLI flags
• Honour hide_progress setting when linting modules (was ignored before)
• Always hide progress bars when using a verbose log

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

[mashehu]

Do we need to update the environment variable in rich-codex.yml with the NFCORE prefix?

[ewels]

Do we need to update the environment variable in rich-codex.yml with the NFCORE prefix?

Looks like that env var is used directly rather than via Click, so no:

tools/nf_core/lint/__init__.py

Line 316 in dec66ab

disable=self.hide_progress or os.environ.get("HIDE_PROGRESS", None) is not None,

[codecov]

Codecov Report

Merging #2016 (b222d89) into dev (d3967e9) will decrease coverage by 0.02%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##              dev    #2016      +/-   ##
==========================================
- Coverage   63.86%   63.84%   -0.03%     
==========================================
  Files          41       41              
  Lines        4926     4923       -3     
==========================================
- Hits         3146     3143       -3     
  Misses       1780     1780              

Impacted Files	Coverage Δ
nf_core/__main__.py	59.36% <100.00%> (-0.23%)	⬇️
nf_core/modules/lint/__init__.py	82.97% <100.00%> (ø)

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