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Template update for nf-core/tools v4.2.1 - #224

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ljwharbers wants to merge 8 commits into

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template_update_4.2.1

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Template update for nf-core/tools v4.2.1#224
ljwharbers wants to merge 8 commits into
devfrom
template_update_4.2.1

Commits on Oct 28, 2026
- Template update for nf-core/tools version 4.2.1
  ljwharbers
  committed
  0ab3233
- Merge nf-core/tools 4.2.1 template into dev
  
  ljwharbers
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  claude
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  4a5ee9c
- Refresh stale extended-test snapshots
  
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  7c6e9fe
- Fill in PR number in CHANGELOG entry
  
  ljwharbers
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  c8db013
Commits on Oct 29, 2026
- Point manifest.diagram at the README metro map
  
  ljwharbers
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  claude
  committed
  ed1ddae
Commits on Nov 2, 2026
- CLAIR3: decide GPU mode from params.use_gpu
  
  ljwharbers
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  claude
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  bd5dace
- CLAIR3: GPU image v2.0.2_gpu -> v2.0.5_gpu
  
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  f1066e4
- Document --use_gpu: every affected tool and the Clair3 GPU limit
  
  ljwharbers
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  0c1cf3f