mag 3.4.0 - Green Gecko

Added

• #745 - Added pipeline parameter spades_downstreaminput to use contigs instead of scaffolds (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi).
• #745 - Added trimmomatic as an additional pre-processing tool (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi).
• #745 - Added parameters for concoct/cut_up_fasta.py including bin_concoct_chunksize, bin_concoct_overlap and bin_concoct_donotconcatlast (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi).
• #777 - Improved input validation through additional JSON keywords and error messages (by @agusinac)

Changed

• #774 - Update CheckM2 to v1.1.0 and default database (by @dialvarezs).

Fixed

• #726 - Fix formatting errors to follow Nextflow best practice (by @dialvarezs).
• #769 - Fix megahit not emitting correct filenames due to suboptimal arguments ordering (reported and fix by @IceGreb)
• #771 - Fix misspecified checkm2 database parameter check (reported by @dpelegri and fix by @jfy133)

Dependencies

Tool	Previous version	New version
CheckM2	1.0.2	1.1.0
SPAdes	4.0.0	4.1.0