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Update nf-core modules and local module tools - #212

Merged

AmberVerhasselt merged 29 commits into

devfrom

chore/module-updates

Oct 2, 2026

Merged

Update nf-core modules and local module tools#212
AmberVerhasselt merged 29 commits into
devfrom
chore/module-updates

Commits on Oct 1, 2026
- Update nf-core modules and bump local module tools
  
  ljwharbers
  and
  claude
  committed
  7eaede8
- Restore NanoPlot arrow input and fix missed .tbi joins
  
  ljwharbers
  and
  claude
  committed
  733bc23
- Rename AF tags only where the source tag exists; update snapshots
  
  ljwharbers
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  claude
  committed
  2ec2bef
- Update union snapshot
  
  ljwharbers
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  claude
  committed
  9555b5c
- Fill in PR number in CHANGELOG entry
  
  ljwharbers
  and
  claude
  committed
  c3ba089
- Update Clair3, ClairS, DeepVariant and DeepSomatic
  
  ljwharbers
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  claude
  committed
  0e628ff
- Restore DeepVariant edits that were missing from the patch files
  
  ljwharbers
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  claude
  committed
  7cb08bb
- Update default, chm13 and clair_only snapshots for the new callers
  
  ljwharbers
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  claude
  committed
  c1d0489
- Update consensus, deep_only and union snapshots for the new callers
  
  ljwharbers
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  claude
  committed
  69ebae2
- Fill in PR number in CHANGELOG entry
  
  ljwharbers
  and
  claude
  committed
  d3d4614
- Skip nf-core component tests in nextflow-lint
  
  ljwharbers
  and
  claude
  committed
  906aad3
- Update Wakhan to 0.5.0
  
  ljwharbers
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  claude
  committed
  6467ebe
- Fill in PR number in CHANGELOG entry
  
  ljwharbers
  and
  claude
  committed
  4f1c7e1
- Correct the #212 CHANGELOG entry
  
  ljwharbers
  and
  claude
  committed
  a47eb1f
- Re-record module snapshots for patched NanoPlot and bcftools
  
  ljwharbers
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  claude
  committed
  9688f05
- Run lrsomatic_report 1.6.1
  
  ljwharbers
  and
  claude
  committed
  786ef8e
- Warn instead of abort on bcftools norm REF mismatches
  
  ljwharbers
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  claude
  committed
  78fb702
- Merge branch 'chore/module-updates' into chore/variant-caller-updates
  ljwharbers
  committed
  a8d27e6
- Address review: DeepSomatic small model, ClairS container ternary
  
  ljwharbers
  and
  claude
  committed
  fc0e823
- Add a WAKHAN module stub test
  
  ljwharbers
  and
  claude
  committed
  1ae5e77
- Merge remote-tracking branch 'origin/chore/module-updates' into feat/wakhan-0.5.0
  ljwharbers
  committed
  2ee7d0a
- Pull WAKHAN from Docker Hub, with the coverage-histogram fix
  
  ljwharbers
  and
  claude
  committed
  9ff6d0c
Commits on Oct 2, 2026
- Merge pull request #213 from IntGenomicsLab/chore/variant-caller-updates
  AmberVerhasselt
  authored
  35b41b4
- Merge origin/chore/module-updates (#213) into feat/wakhan-0.5.0
  
  ljwharbers
  and
  claude
  committed
  9edfb76
- Merge pull request #214 from IntGenomicsLab/feat/wakhan-0.5.0
  AmberVerhasselt
  authored
  f8a8dc5
- Address round-2 review: CLAIR3_MODEL TLS, stub test, model checks
  
  ljwharbers
  and
  claude
  committed
  30d5cc6
- Merge dev into chore/module-updates
  
  ljwharbers
  and
  claude
  committed
  5060eb8
- Regenerate snapshots after merging dev
  
  ljwharbers
  and
  claude
  committed
  f74b247
- Merge branch 'dev' into chore/module-updates
  
  ljwharbers
  and
  claude
  committed
  e5284ea

Commits

Commits on Oct 1, 2026

Commits on Oct 2, 2026