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Make the pipeline a typed pipeline that can be included in another pipeline - #758

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feat/pipeline-composition

Commits on Oct 1, 2026
Commits on Oct 2, 2026
- Trigger CI for review
  
  pinin4fjords
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  claude
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  16e96b8
- ci: give the nf-core lint the patched nf-schema repository; patch the vendored subworkflows that differ from upstream
  
  pinin4fjords
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  claude
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  32daba7
Commits on Oct 5, 2026
- Switch the report to the quarto/notebook module [skip ci]
  
  pinin4fjords
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  claude
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  8152039
- Point the report process config at QUARTO_NOTEBOOK [skip ci]
  
  pinin4fjords
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  claude
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  23bfce2