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Added myloasm as an alternative assembler - supply --assembler myloasm to select it.
Added a pipeline logo.
Fixed
Updated metaMDBG to 1.3.1, improving the quality of output assemblies.
Dependencies
module
tools
old versions
new versions
metamdbg
metamdbg
1.2.0
1.3.1
myloasm
myloasm
-
0.5.1
gtdbtk/classifywf
gtdbtk
2.5.2
2.6.1
[1.3.2] - Glasgow Peggie (patch 2) - [2025-03-31]
Added
Pipeline now supports input of fastq files for long reads.
Fixed
Move pipeline code to Nextflow strict syntax
Deprecated
Dependencies
module
tools
old versions
new versions
genomad/endtoend
genomad
1.11.0
1.11.2
[1.3.1] - Glasgow Peggie (patch 1) - [2025-11-29]
Fixed
Correctly emit the versions from the FASTX_MAP_LONG_READS subworkflow. (by @prototaxites)
[1.3.0] - Glasgow Peggie - [2025-11-28]
Added
Switch the read mapping and Hi-C mapping to use the new sanger-tol subworkflows. (by @prototaxites)
gunzip all assemblies and operate on assemblies in decompressed space internally. (by @prototaxites)
Operate on decompressed assemblies downstream to avoid lack of bgzipping. (by @prototaxites)
Fixed
Sometimes MAGScoT fails, for unknown reasons. The pipeline will no longer exit if this happens. (by @prototaxites)
If no circular contigs are found, a FASTA file will no longer be written and GeNomad will no longer run (and fail). (by @prototaxites)
Change the minimum percent identity during read mapping to 99% to reflect accuracy of PacBio reads. (by @prototaxites)
Deprecated
Removed the parameter params.hic_mapping_merge_mode, as we now use the new Hi-C mapping subworkflow. (by @prototaxites)
Removed the parameter params.enable_assembly - assembly now always runs by default unless an assembly is provided. (by @prototaxites)
Dependencies
module
tools
old versions
new versions
gunzip
gzip
-
1.13
gzip_get_decompressed_size
gzip
1.13
-
fastxalign/pyfastxindex
pyfastx
-
2.2.0
fastxalign/minimap2align
pyfastx
-
2.2.0
fastxalign/minimap2align
minimap2
-
2.30
fastxalign/minimap2align
samtools
-
1.22.1
cramalign/gencramchunks
-
-
1.1.0
cramalign/bwamem2align
bwa-mem2
-
1.22.1
cramalign/bwamem2align
samtools
-
1.22.1
cramalign/minimap2align
minimap2
-
2.30
cramalign/minimap2align
samtools
-
1.22.1
minimap2/align
minimap2
2.2.9
-
minimap2/align
samtools
1.21
-
samtools/sort
samtools
-
1.22.1
samtools/mergedup
samtools
-
1.22.1
samtools/faidx
samtools
-
1.22.1
samtools/splitheader
samtools
-
1.22.1
[1.2.1] - Fair Margaret and Sweet William (patch 1) - [2025-10-24]
Added
Fixed
tRNAScan-SE summary now correctly calculates the total number of tRNA hits (by @prototaxites)
Deprecated
Dependencies
[1.2.0] - Fair Margaret and Sweet William - [2025-09-23]
Added
Pipeline-level nf-test implemented - update to template 3.3.2 (by @prototaxites)
GTDB-Tk updates:
Update GTDB-Tk to 2.5.2 to fix conda env issues (by @prototaxites)
Remove patch from gtdbtk/classifywf module and switch to the new gtdbtk/gtdbtoncbimajorityvote module to convert to NCBI taxonomy (by @prototaxites)
Added gtdbtk_use_full_tree parameter. This is enabled in the nf-test tests to allow use of the mock DB, but if enabled using the full GTDB-Tk
db, all bacterial bins will be placed into the full bacterial tree. This requires >=320 GB of memory (by @prototaxites)
Added gtdbtk_skip_ani_screen parameter. This is also enabled in the nf-test tests to allow use of the mock DB. Skips running the ANI pre-screen step using skani for classification without using marker genes (by @prototaxites)
Join NCBI classifications to GTDB-Tk summary and output this file instead (by @prototaxites)
GTDB classification method included in bin summary (by @prototaxites)
Return free-disk-space to nf-test CI runners (by @prototaxites)
Emit all contig2bin files in the output directory (by @prototaxites)
Include filename in bin_summary.tsv results file (by @prototaxites)
Add extra output TSV file with per-contig information (length, GC, circularity) (by @prototaxites)
Use nf-core infernal/cmsearch module (by @prototaxites)
Estimate bin coverage with coverm/genome (by @prototaxites)
(Sanger internal use) - add a Tree of Life Assembly profile to configure access to databases (by @prototaxites)
Fixed
Fixed bug where Metator bin FASTA files were not being published (by @prototaxites)
Fixed bug where bin3C bins were not being passed to GTDB-Tk due to a silently failing join (by @prototaxites)
Fixed bug where coverm contig depths were not being published (by @prototaxites)
Ensure contig2bins are always tab-separated and have tsv ending (by @prototaxites)
Updated all out-of-date nf-core modules (by @prototaxites)
Relax Nextflow version dependency after bugfix (by @prototaxites)
Fixed bug where the BIN_SUMMARY process would run if binning was disabled (by @prototaxites)
Deprecated
Removed the code that automatically downloads the CheckM2 and Genomad databases if they are not provided, as these can now
be specified for download in the nf-test setup block and are thus not required (by @prototaxites)
Removed TaxonKit - the code for generating submittable taxnames/taxids did not work well (by @prototaxites)
Removed gtdbtk_mash_db parameter as it is now deprecated (by @prototaxites)
Dependencies
module
tools
old versions
new versions
metamdbg/asm
metamdbg
1.1
1.2
gtdbtk/classifywf
gtdbtk
2.4.0
2.5.2
gtdbtk/gtdbtoncbimajorityvote
gtdbtk_to_ncbi_majority_vote
-
0.2.1
minimap2/align
minimap2
2.28
2.29
minimap2/align
samtools
1.20
1.21
taxonkit/name2taxid
taxonkit
0.15.1
-
samtools/merge
samtools
1.21
1.22.1
samtools/index
samtools
1.21
1.22.1
nextflow
nextflow
25.04.02
24.04.02
[1.1.1] - The Elfin Knight (patch 1) - [2025-06-02]
Fixed
Fixed bug where single-file inputs to metaMDBG caused a file-not-found error (by @prototaxites)
Upgrade Metator to avoid bug in Conda
Dependencies
module
tools
old versions
new versions
metator/pipeline
metator
1.3.7
1.3.10
nextflow
nextflow
24.04.02
25.04.02
[1.1.0] - The Elfin Knight - [2025-04-14]
Added
Adds genomad for classification of circular contigs to determine whether they are plasmids (by @prototaxites)
adds --enable_genomad to turn on and off this step (enabled by default)
adds --genomad_splits to control memory usage - increasing this value from the default 1 increases
chunking of the genomad database, reducing memory usage at the cost of increased runtime
Fixed
Fixed missing output channel in gtdbtk/classifywf (by @prototaxites)
Add in some previously-excluded parts of the template (by @prototaxites)
Post-release fix - the actual license at this stage is GPL-3.0.
v1.0.0 and v1.0.1 should be considered GPL-3.0 as well, despite the wrong LICENSE file.
Initial release of sanger-tol/metagenomeassembly, created with the nf-core template.
Added
All added by @prototaxites, reviewed by @DLBPointon, @weaglesBio, @ksenia-krasheninnikova:
Raw assembly of PacBio reads with metaMDBG.
Mapping of PacBio reads to assembly with minimap2
Estimation of contig mean coverages with coverm
Chunked mapping of Hi-C reads to assembly with bwa-mem2
Binning with:
Metabat2
MaxBin2
Bin3C (Hi-C)
Metator (Hi-C)
Bin refinement with:
DAS_Tool
MagScoT
Assembly and bin QC:
Seqkit stats - size, N50, etc.
Counts of circular contigs
rRNA (5S, 16S, 18S) identification and counting
Bin QC only:
Assessing bin completeness and contamination with CheckM2
Assessing tRNA content of bins with tRNAScan-SE
Bin taxonomic assignment:
GTDB-Tk for taxonomic classification
TaxonKit to convert GTDB-Tk taxonomic classifications to NCBI
Per-bin and aggregated summaries
Fixed
Dependencies
Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.