NBISweden/AGAT: AGAT v1.6.0

Major Release

This release introduces significant improvements in performance, usability, and code maintainability.

Enhancements • Several method optimizations resulting in small performance gains. • Input processing parallelization is now available via the new cpu parameter. The input file is split into agat_tmp chunks by sequence identifier, and each chunk is processed using Parallel::ForkManager. This improves performance only when the number of sequences is greater than or equal to the number of CPUs and when input files are large (>300 MB). The original single-CPU behavior can be restored using cpu=0. • Unified CLI options: --output, --out, and -o are now equivalent (outfile removed). • Unified boolean option handling: --boolean_option enables the option. --no-boolean_option disables it (as handled by the agat script. But note that scripts only suggest boolean activation). • Centralized all printing via the dual_print method. • Centralized key information using global variables to simplify method calls (no need to pass numerous variables). These are defined in Utilities.pm. • Configuration CONFIG is now populated earlier and is accessible globally. • hashID and mRNAGeneLink are now included in the omniscient hash to simplify data access and method calls. • Gzipped files are now processed directly in Perl, improving compatibility with Windows. • Added a Nextflow pipeline to assess performance.

•	Test suite parallelization.
•	Scripts are now pipe-safe.
•	Unified CLI through shared options (aligned with agat_config.yaml). All AGAT configuration options can now be set directly from the command line.

The last three points were inspired by and benefited from #559. Many thanks to @kim-fehl for the contribution.

Bug Fixes • Fix #556: prevent empty attributes from being concatenated to ID during GFF3 parsing. • Fix #250: preserve URL-escaped characters in the output. • Fix #507: add a raw option to export raw data into a dedicated folder for agat_sp_statistics.pl.

New Options • Added url_encode_out parameter to decode URL-escaped characters in GFF3 output (usefulness to be evaluated). • Added --force option to overwrite existing output files.

Documentation • Homogenized POD documentation (option types now specified in the options line, e.g. -o, --out, --output <file>). • Simplified the second part of the POD across all scripts.

Full Changelog: https://github.com/NBISweden/AGAT/compare/v1.5.1...v1.6.0