nf-core/pairgenomealign v2.0.0 – Naga imo

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).