metagenomeassembly - v1.1.1 - The Elfin Knight (patch 1)

[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 |

- Nextflow
Published by prototaxites 9 months ago

metagenomeassembly - v1.1.0 - The Elfin Knight

[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)

Dependencies

| module | tools | old versions | new versions | | ---------------- | -------------------- | ------------ | --------------------- | | find_circles | seqkit,samtools,gawk | 2.9.0, -, - | 2.10.0, 1.21.0, 5.3.0 | | genomad/download | genomad | - | 1.11.0 | | genomad/endtoend | genomad | - | 1.11.0 |

Deprecated

- Nextflow
Published by prototaxites 11 months ago

metagenomeassembly - v1.0.3 - Scarborough Fair (patch 3)

[1.0.3] - Scarborough Fair (patch 3) - [2025-04-08]

• Relicensed this repository as MIT
• Updated the GTDB-Tk container to a sanger-tol container that has both GTDB-Tk and the gtdbtoncbimajorityvote.py script (by @prototaxites)
  • Minor change to GTDB database channel preparation to reflect new changes to the nf-core module (by @prototaxites)

- Nextflow
Published by prototaxites 11 months ago

metagenomeassembly - v1.0.2 - Scarborough Fair (patch 2)

[1.0.2] - Scarborough Fair (patch 2) - [2025-04-08]

Post-release fix - the actual license at this stage is GPL-3.0 or later. v1.0.0 and v1.0.1 should be considered GPL-3.0 as well, despite the wrong LICENSE file.

- Nextflow
Published by muffato 11 months ago

metagenomeassembly - v1.0.1 - Scarborough Fair (patch 1)

[1.0.1] - Scarborough Fair (patch 1) - [2025-03-31]

Post-release fix - adds Zenodo release to pipline code.

Note: this version should be considered as licensed under GPL-3.0 (or later) rather than MIT. Ignore the wrong LICENSE file.

Added

• Add Zenodo DOI (10.5281/zenodo.15090769) to README.md, CITATION.cff and nextflow.config (by @prototaxites)
• Add pretty sanger-tol logo to --help output (by @muffato)

Fixed

• Fix ci.yml to correctly trigger on main rather than master (by @prototaxites)
• Fix schema $id path in assets/schema_input.json (by @prototaxites)
• Conda fixes:
  • Add missing environment.yml reference to cramfilterbwamem2alignfixmate_sort (by @prototaxites)
  • Add explicit catch in binning subworkflow to only run Bin3C and MagScoT if conda is not enabled (by @prototaxites)
  • Update metator to ensure conda works correctly (by @prototaxites)

Dependencies

| module | tools | old versions | new versions | | ---------------- | ------- | ------------ | ------------ | | metator/pipeline | metator | 1.3.2 | 1.3.7 |

Deprecated

- Nextflow
Published by prototaxites 11 months ago

metagenomeassembly - v1.0.0 - Scarborough Fair

[1.0.0] - Scarborough Fair - [2025-03-26]

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.

| module | tools | old versions | new versions | | -------------------------------------- | --------------------------------- | ------------ | ------------------- | | binrrnas | gawk | - | 5.3.0 | | binsummary | r-base, r-tidyverse | - | 4.4.2, 2.0 | | bin3c/mkmap | bin3c, gzip, ngzip | - | 0.3.3 | | bin3c/cluster | bin3c, gzip, ngzip | - | 0.3.3, 1.9. 1.9 | | bwamem2/index | bwa-mem2 | - | 2.2.1 | | checkm2predict | checkm2 | - | 1.0.2 | | checkm2databasedownload | aria2 | - | 1.36.0 | | contig2bintofasta | seqkit | - | 2.9.0 | | coverm/contig | coverm | - | 0.7 | | cramfilterbwamem2alignfixmatesort | stadeniolib, samtools, bwa-mem2 | - | 1.15.0, 1.21, 2.2.1 | | dastool/dastool | dastool | - | 1.1.7 | | findcircles | gawk | - | 5.3.0 | | gawk | gawk | - | 5.3.0 | | genomestats | seqkit | - | 2.9.0 | | gtdbtk/classifywf | gtdb-tk | - | 2.4.0 | | gzipgetdecompressedsize | gzip | - | 1.13 | | hmmer/hmmsearch | hmmer | - | 3.4 | | infernal/cmsearch | infernal | - | 1.1.5 | | magscot/magscot | magscot | - | 1.1.0 | | maxbin2 | maxbin2 | - | 2.2.7 | | metabat2/metabat2 | metabat2 | - | 2.17 | | metamdbg | metamdbg | - | 1.1 | | metator/pipeline | metator | - | 1.3.2 | | metator/processinputbam | samtools, bioawk | - | 1.21, 1.0 | | minimap2 | minimap2, samtools | - | 2.28, 1.21 | | pyrodigal | pyrodigal | - | 3.6.3 | | samtools/mergehicbam | samtools | - | 1.21 | | samtoolscatsort | samtools | - | 1.21 | | taxonkit/name2taxid | taxonkit | - | 0.15.1 | | trnascan_se | trnascan-se | - | 2.0.12 |

- Nextflow
Published by prototaxites 11 months ago