Added

• #905 - Add nf-test snapshot for test_assembly_input profile (by @dialvarezs)
• #930 - Add binner SemiBin2 (by @d4straub)
• #861 - Added --generate_bigmag_file to execute the bigmag workflow that generates the file to be used as input for BIgMAG (added by @jeffe107)

Changed

• #932 - Replaced usages of deprecated Channel() with channel() and fix other LSP warnings (by @dialvarezs)
• #937 - Updated to nf-core 3.5.1 TEMPLATE (by @dialvarezs)
• #938 - Update nf-core modules (by @dialvarezs)

Fixed

• #894 - Fix read order in metaSPAdes to allow co-assembly of paired-end data of multiple samples (reported by @maartenciers, fix by @jfy133 with contributions from @prototaxites, @d4straub and @dialvarezs)
• #927 - MetaBinner now succeeds when no contigs are too short or all are binned (reported by @MicroSeq, fix by @d4straub)
• #929 - Allow the domain_classification.R script to run with any assembler, not just Megahit or Spades (reported by @MicroSeq, fix by @prototaxites)
• #943 - Fixed concatenation of BUSCO summaries with uneven columns by changing from csvtk to qsv (reported by @jfy133 and @julianu, fix by @dialvarezs)
• #943 - Fixed creation of the Tiara report channel used for concatenation (by @dialvarezs)
• #945 - Skip mixing of GTDB-Tk MultiQC files when binning is skipped (reported by @amizeranschi, fix by @dialvarezs)
• #953 - metaSPAdes retries upon error 250 (out of memory), rather than finishing the pipeline.
• #954 - Skip GTDB-Tk when no bin QC tool is enabled and add warning messages (fix by @dialvarezs)
• #956 - Support long reads assemblers in assembly input (fix by @dialvarezs)

Dependencies

Deprecated

• #943 - Remove csvtk/concat module (by @dialvarezs).