v2.2.0 “Chagara ponzu” - [May 29th 2025]

Added

• Support for export to BAM and CRAM formats (#31) (#43).
• SAM/BAM/CRAM alignments files are sorted and their header features all sequences of the target genome.
• Report ungapped percent identity (#46).
• Update full-size test genomes to feature more T2T assemblies (#59).
• Use a single mulled container for LAST, Samtools and open-fonts, to save ~280 Mb of downloads (#58).
• Allow export to multiple formats (comma-separated list) (#42).
• Allow skipping of the assembly QC with --skip_assembly_qc (#53).

Dependencies

Parameters

Fixed

• Remove noisy tag in the MULTIQC_ASSEMBLYSCAN_PLOT_DATA local module (#64).
• Restore BED format support (#56).
• Document the multiqc_train.txt and multiqc_last_o2o.txt aggregating alignment statistics (#52).
• Point the test configs samplesheets to nf-core/test-datasets in order to run the AWS full tests (#62).
• Update metro map, in white background (#71).
• Removed the last/mafswap module, which was actually not used.

v2.1.0 “Goya champuru” - [May 16th 2025]

Added

• New --dotplot_filter paramater to produce extra alignment plots where small off-diagonal signal is filtered out (#35).
• New --dotplot_width, --dotplot_height and --dotplot_font_size parameters to control alignment plot size (#38).

Fixed

• In alignment plots, contig names are now written with a nice scalable font instead of being pixellised (#44).
• Conforms to nf-core template version 3.2.1 (#54).
• Removed some old linting exceptions.
• Removed the gfastats modules, which was actually not used.
• Make sure the subworkflows collect all module versions.
• Fix plot IDs for comptatibility with MultiQC 1.28.

Parameters

Dependencies

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.

In retrospect it was found that this version (only) is not compatible with Nextflow 25.04 or higher. Please use v1.1.0 instead if you need the same functionality and software version numbers.

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.