v2.4.0

What's Changed

• QC process has been changed to include results of GTDB-Tk in the genome filtering process. Genomes that cannot be assigned to a taxonomic domain by GTDB-Tk are now filtered out.
• GTDB-Tk version updated to 2.4.0 and GTDB database updated to R220.
• New annotations added: BGC detection by GECCO and antiSMASH, putative PULs and CAZy annotations by run_dbcan, anti-phage defense system annotation by Defense Finder, KEGG pathway completeness information by MGnify's pathway completeness tool.
• Added tax scope to the eggNOG mapper command (prokaryota_broad).
• Added an e-value filter when adding eggNOG and InterProScan annotations to the final genome annotation GFF file.
• Changed tRNA detection algorithm from cmscan to tRNAscan-SE only. Previously tRNAscan-SE was only used to get the tRNA count while the records in the GFF file were generated based on cmscan results.
• Genome fetching script now includes a --skip-filter option to skip filtering genomes by their completeness and contamination.
• Added a post-processing script that cleans up mobilome files if no results were detected by the mobilome pipeline.

Full Changelog: v2.3.0...v2.4.0

v2.3.0

What's Changed

• Changed completeness/contamination tool from CheckM to CheckM2 by @tgurbich and @mberacochea in #95
• Added an e-value filter when incorporating InterPro and eggNOG matches into the annotation GFF, removed addition of empty values, added GO-terms from eggNOG and minor bug fixes by @tgurbich in #90
• Switched tree generation tool from IQ-Tree to FastTree if the number of species representatives in a domain is >=2000 by @tgurbich and @mberacochea in #93 and #96
• Added the --cpu flag for Sanntis by @mberacochea in #86
• Minor adjustments to run the pipeline in Codon + Slurm by @mberacochea in #91
• Update genome fetching script by @tgurbich in #92
• Fixes and support for compressed genomes in the deduplication script by @KateSakharova in #94
• Added changes to GTDB output for unclassified genomes to preserve the format by @tgurbich in #93
• Enabled pre-determined genome accessions by @tgurbich in #93
• Fixed a bug in the README generation script to correctly account for Archaea by @tgurbich
• Memory requirement adjustments by @KateSakharova

Full Changelog: v2.2.1...v2.3.0

v2.2.1

What's Changed

• Update README.md: fix dead links to download files by @KateSakharova in #75
• Bug fix/organising script by @tgurbich in #74
• Merge dev to a new release by @mberacochea in #78

Full Changelog: v2.2.0...v2.2.1

v2.2.0

What's Changed

• Added support for extra-large catalogues (>25k genomes) which is implemented by replacing the dereplication step with chunked dereplication.
• Added generation of RNAcentral import files.
• Added gzipping of the gene catalogue.
• Bug fix: removed splitting scaffolds into contigs when calculating contig number for the metadata table.

Full Changelog: v2.1.1...v2.2.0

MAGs pipeline v2.1.1

What's Changed

• Added a file organiser script by @tgurbich in #44
• Bugfix: fixed path to modules by @tgurbich in #45
• Extra weight table generation can now consider user-provided isolate info by @mberacochea in #46
• Added fixes to account for missing data in ENA by @tgurbich in #48
• Fixed conditions for IQtree generation by @mberacochea in #49
• Metadata fetching scripts fixes and improvements by @tgurbich in #51

Full Changelog: v2.1.0...v2.1.1

MAGs pipeline v2.1.0

What's Changed

• Change base image for GTDB-tk 2.3.0 by @mberacochea in #41
• V2.1.0 by @mberacochea in #42
• v2.1.0 by @mberacochea in #43
• InterProScan, GTDB, RFam and eggNOG version update @tgurbich

Code review: @Ales-ibt

Full Changelog: v2.0.1...v2.1.0

MAGs pipeline v2.0.1 - BUGFIX release

Fix for the GUNC step, it was not reporting the gunc_failed.txt

Full Changelog: v2.0.0...v2.0.1

MAGs pipeline v2.0.0

First release of the nextflow version of the pipeline

What's Changed

• Migration to nextflow by @mberacochea in #34
• Feature/add qs50 filtering by @KeteSakharova in #36
• Feature/repo cleaning EMG-4395 by @mberacochea in #39
• Tools and multiples fixes by @tgurbich

Full Changelog: v1.3.1...v2.0.0

MAGs pipeline v1.3.1

This pre-release contains small fixes on paths and scripts for v1.3.0

This is a pre-release, we are working to improve the portability of the pipeline.

MAGs pipeline v1.3.0

Source env in run.sh