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Cram#41

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Juke34 merged 8 commits intomainfrom
cram
Feb 5, 2026
Merged

Cram#41
Juke34 merged 8 commits intomainfrom
cram

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@Juke34
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@Juke34 Juke34 commented Feb 4, 2026

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Juke34 commented Feb 5, 2026

This PR Fix #40

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Juke34 commented Feb 5, 2026

This PR fix:

  • Add cram output
  • Add Index to bam/cram output
  • Missing output when running subread
  • Kallisto output is now sorted
  • Update to latest samtools version
  • nglmr => paired output was missing
  • fix displayed tag into bwamem2

@Juke34 Juke34 merged commit 378bd22 into main Feb 5, 2026
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