mag 4.0.0 - Blue Huemul

Added

• #730 - Added --busco_db_lineage to allow specifying a specific lineage for BUSCO database (added by @jfy133, @dialvarezs)
• #730 - Added a new documentation section on database setup (by @jfy133, @dialvarezs)
• #784 - Added --bin_min_size and --bin_max_size parameters to filter out bins based on size (requested by @maxibor, @alexhbnr, added by @jfy133, @prototaxites)
• #793 - Document use of a SquashFS image with --gtdb_db, useful for limited inode infrastructure (by @muniheart)
• #805 - Add support for fastp's --trim_poly_g option (by @jfy133)

Changed

• #730 - Migrate from local BUSCO module to nf-core one, updating version (by @dialvarezs)
• #730 - Use BUSCO database from nf-core test datasets (by @dialvarezs)
• #788 - Tweak method of loading GTDB database in GTDBTK_CLASSIFYWF for more stability (reported by @alexhbnr, fix by @jfy133)
• #800 - Default branch is now set to main (by @jfy133 and @mirpedrol)
• #801 - Increase CheckM memory requests to match recommended requirements (by @jfy133)

Fixed

• #789 - Improve --bowtie2_mode description to clarify default settings (reported by @IceGreb, fix by @jfy133)
• #798 - Fix overly strict database validation for --metauk_db and improve documentation (reported by @ruqse, fix by @jfy133)
• #804 - Fix broken memory specification for FASTQC (reported by @jmichaelegana, fix by @awgymer & @jfy133)

Dependencies

Tool	Previous version	New version
BUSCO	5.4.3	5.8.3
csvtk		0.31.0
nextflow	24.04.2	25.04.2

Deprecated

• #730 - Remove --busco_auto_lineage_prok due to update and simplified usage of BUSCO (added by @jfy133, @dialvarezs)