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Fix/downgrade mosdepth#336

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matthdsm merged 5 commits into
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fix/downgrade_mosdepth
Jun 4, 2026
Merged

Fix/downgrade mosdepth#336
matthdsm merged 5 commits into
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fix/downgrade_mosdepth

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@matthdsm

@matthdsm matthdsm commented Jun 4, 2026

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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@matthdsm matthdsm linked an issue Jun 4, 2026 that may be closed by this pull request
Mosdepth failure on contig mismatch between cram and fasta #335
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@matthdsm matthdsm requested review from ToonRosseel and nvnieuwk June 4, 2026 08:18
jhaezebr
jhaezebr approved these changes Jun 4, 2026
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Looks like a decent downgrade to me

@matthdsm matthdsm merged commit 52d88e6 into dev Jun 4, 2026
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@matthdsm matthdsm deleted the fix/downgrade_mosdepth branch June 4, 2026 11:42
@matthdsm matthdsm mentioned this pull request Jun 4, 2026
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matthdsm added a commit that referenced this pull request Jun 6, 2026
@matthdsm
nf-cmgg/smallvariants v1.13.3 (#340)
ce0e506 
* Bump bcftools modules (#338)
* downgrade mosdepth (#336)
* bump pipeline version (#339)
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@jhaezebr jhaezebr jhaezebr approved these changes
@nvnieuwk nvnieuwk Awaiting requested review from nvnieuwk
@ToonRosseel ToonRosseel Awaiting requested review from ToonRosseel

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Mosdepth failure on contig mismatch between cram and fasta

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@matthdsm @jhaezebr