Sync matrix

[ewels]

Refactored sync code:

• Use GitHub actions job matrix to have separate actions jobs for each pipeline [closes Sync all: use GitHub Actions matrix #673]
  • This uses a list of pipelines on the website which does not include archived pipelines [closes Sync - ignore archived pipelines #712]
  • x-ref Make pipeline_names.json website#483
• New code lists existing PRs and tries to update the title and body if one found [closes Sync - recognise existing PRs and treat as success #710]

Still TODO:

• Update tests for new sync code
• Run manual sync commands on pipelines with and without existing template PRs to check that it works in real life

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 #716 into dev will increase coverage by 1.11%.
The diff coverage is 71.42%.

@@            Coverage Diff             @@
##              dev     #716      +/-   ##
==========================================
+ Coverage   81.92%   83.04%   +1.11%     
==========================================
  Files          13       13              
  Lines        2766     2748      -18     
==========================================
+ Hits         2266     2282      +16     
+ Misses        500      466      -34     

Impacted Files	Coverage Δ
nf_core/__main__.py	62.92% <40.00%> (+1.10%)	⬆️
nf_core/sync.py	75.52% <77.35%> (+12.64%)	⬆️

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[ewels]

Manual test with methylseq worked: nf-core/methylseq#165 (no existing PR)

[ewels]

Manual test with ampliseq also worked! nf-core/ampliseq#134 (comment) (existing PR updated)

[ewels]

Just tested again manually with methylseq and ampliseq, in addition to mag earlier with the fixed 404s. All looking good!

[drpatelh]

Nice! LGTM!