nf-core/pairgenomealign: nf-core/pairgenomealign v3.0.2 – Tokoroten shiki

v3.0.2 "Tokoroten shiki" - [July 16th 2026]

This is a bugfix release, please make sure you also look at the 3.0.1 and 3.0.0 entries in the changelog.

Fixed

• Restore maximum tandem repeat unit length to 400 for genome masking, to prevent running out of memory on centromeric repeats. LASTs default changed to 100 in version 1638, causing a regression in this pipeline's v3.0.0 release (#139)
• Restore missing fasta in the target genome name indexed for CRAM files (#140).
• Avoid collisions by adding .cuts to the name of the file defining the regions of more than 10 Ns in the target genome. (#138).
• Fix blasttab+ export option by correcting Nextflow schema. Thanks, @sapunyangkut (#141).
• Fix blasttab+ format by upgrading LAST to version 1652 (no other changes). For consistency, Samtools and Bcftools were also upgraded (no visible changes expected).

Dependencies

| Dependency | Old version | New version | | ---------- | ----------- | ----------- | | LAST | 1651 | 1652 | | BCFTOOLS | 1.23.1 | 1.24 | | SAMTOOLS | 1.23.1 | 1.24 |