v2.0.0 “Naga imo” - [February 5th, 2025]

Breaking changes

• The LAST software was updated and it has new defaults for some of its parameters. The alignments ran with this pipeline will not be identical to the ones from older versions.

Added

• The alignment/lastdb directory is not output anymore. It consumed space, is not usually needed for downstream analysis, and can be re-computed identically if needed.
• The many-to-one alignment file is not output anymore by default, to save space. To keep this file, you can run the pipeline in many-to-many mode with the --m2m parameter.
• The --seed parameter allows for all the existing values in the lastdb program.
• Errors caused by absence of alignments at training or plotting steps are now ignored.
• New parameter --export_aln_to that creates additional files containing the alignments in a different format such as Axt, Chain, GFF or SAM.

Fixed

• Incorrect detection of regions with 10 or more Ns was corrected (#18).
• The --lastal_params now works as intended instead of being ignored (#22).
• The workflow summary is now properly sorted at the end of the MultiQC report (#32).
• Conforms to nf-core template version 3.2.0 (#40).

This release brings the pipeline to the standards of Nextflow 24.10.1 and nf-core 3.1.0. No changes were made to the alignment process.

Added a new softmask parameter, to optionally keep original softmasking.

Initial release. Thanks again to my colleagues, collaborators, and the nf-core community.

nf-core/pairgenomealign is a bioinformatics pipeline that aligns one or more query genomes to a target genome, and plots pairwise representations.