v1.5.0 - Polly on the Shore

[1.5.0] - Polly on the Shore - [2026-09-03]

Added

• #95 Circular contig extraction (by @prototaxites)
  • Circular contigs above a given size are now treated as complete genomes. This can be disabled by setting --extract_circular_contigs false.
  • The threshold for circular contig minimum size can be configured with --minimum_circular_contig_length
• Hi-C BAM is now converted to a pairs file, which is fed into Metator
• #96 Add three new binners - ComeBin, SemiBin2, and VAMB.
• #98 Allow filtering of assembled contigs by size (--min_contig_length, --max_contig_length), as well as by Tiara classification (--tiara_exclude_classifications) if Tiara is run (--enable_tiara).
• #98 Add binning with TaxVAMB. This uses contig-level taxonomic classifications classified by Centrifuge - a centrifuge DB must be supplied to --centrifuge_db.
• #98 GTDBTk updated to 2.7.2. This requires the new r232 database.
  • The --gtdbtk_skip_ani_screen parameter has been replaced with the --gtdbtk_place_species parameter.
• #100 Added bin refinement with Binette, which can be enabled with --enable_binette. Binette uses the Checkm2 database, and thus the --checkm2_db parameter is required.

Fixed

• #95 Remove all references to params outside the entry subworkflow (by @prototaxites)
• #95 tRNAscan-SE now runs once per assembly rather than for each bin. The results are aggregated as with the rRNA results (by @prototaxites)
• #96 MaxBin2 is now disabled by default.
• #96 The hic: cram: enzymes: section of the samplesheet is deprecated - please supply enzymes as an optional comma-separated list of enzymes to --hic_enzymes.
• #99 Update to nf-core template version 4.1.0.
  • Note that this update removes the existing Teams and Slack notification functionality. If you were using this functionality, please configure the nf-slack or nf-teams Nextflow plugins.
• #100 Modules updated to their latest versions.

Removed

• #95 Bin3C is now deprecated. It was not maintainable, as it depended on a container provided by the developer (by @prototaxites)
• #100 MagScoT has been removed from the pipeline as it did not provide satisfactory results and was not compatible with Conda (by @prototaxites)

Dependencies

module	tools	old versions	new versions
bin3c/mkmap	bin3c	0.3.3	-
bin3c/cluster	bin3c	0.3.3	-
binette	binette	-	1.2.1
csvtk/concat	csvtk	0.31.0	0.37.0
csvtk/join	csvtk	0.31.0	0.37.0
centrifuger/centrifuger	centrifuger	-	1.1.2
centrifuger/lineage	centrifuger	-	1.1.2
comebin/runcomebin	comebin	-	1.1.0
gtdbtk/classifywf	gtdbtk	2.6.1	2.7.2
gtdbtk/gtdbtoncbimajorityvote	gtdbtk	2.6.1	2.7.2
metamdbg/asm	metamdb	1.3.1	1.4.0
myloasm	myloasm	0.5.1	0.6.0
pairtools/parsefiltersort	pairtools	-	1.1.3
ripgrep	ripgrep	-	14.1.1
tiara/tiara	tiara	-	1.0.3
samtools/faidx	samtools	1.23.1	1.24
samtools/index	samtools	1.23.1	1.24
samtools/merge	samtools	1.23.1	1.24
samtools/splitheader	samtools	1.23.1	1.24
semibin/singleeasybin	semibin	-	2.4.1
seqkit/replace	seqkit	2.9.0	2.13.0
seqkit/split2	seqkit	2.9.0	2.13.0
vamb/bin	vamb	-	5.0.4