nf-core/pairgenomealign: nf-core/pairgenomealign v3.0.0 – Tokoroten

v3.0.0 "Tokoroten" - [June 26th 2026]

Breaking changes

• Simplify output file names by removing _aln and _plt.
• Update all modules to latest versions.
• Use the default CRAM format from samtools (CRAM v3.1 as of samtools 1.23.1) (#86).
• Make bigger plots, and orient sequence names vertically for the target genome (#118).
• Increase the symmetry of the alignment by passing --gapsym and --matsym to last-train (#91).
• Change default seed from YASS to RY4 (#121).
• Move target genome information from cutn to targetgenome (#126).

Added

• Extract a substitution matrix from the alignment and compute evolutionary distance indices (#102).
• Allow FASTQ query input (#122).
• Updated last/mafconvert to allow BCF output, and updated the module diffs so that the shared container also includes BCFtools. BCF output is experimental and output may change in minor revisions of the pipeline (#82).
• Index BCF and CRAM files (#115).

Fixed

• Compatible with Nextflow 26.04 "strict syntax" (#120).
• Merge target and query genome information in a single channel (#119).
• Replace self-alignment with alignment to a different genome in the CI tests (nf-core/test-datasets#122).
• Add back alignment training and result statistics that slipped out of MultiQC in version 2.3.0 (#124).
• Fix erroneous doubling of the reported length and number of sequences of the target genome when both strands are indexed (#128).

Dependencies

| Dependency | Old version | New version | | ---------- | ------------- | ------------- | | LAST | 1611 | 1651 | | BCFTOOLS | | 1.23.1 | | SAMTOOLS | 1.21 / 1.23.1 | 1.23.1 (only) | | MultiQC | 1.34 | 1.35 |