v2.13.1

Full Changelog: v2.12.1...v2.13.1

2.13.1

• Breaking change: New Docker image.
• Added amrfinder, removed abricate.
• Added text hints.
• Add version info to report.
• New checkpoint system that uses file testing and failures instead of the built in checkpoint system which turned out to not be working correctly. @AstaLaugesen
• Deeper CI tests on GitHub Actions.

v2.12.1

Full Changelog: v2.11.2...v2.12.1

2.12.1

• Breaking change: New Docker image.
• Remove anaconda and defaults channels from worklow conda envs.
• Rule "all" inputs are now set by the number of input genomes.
• Added --downloads functionality. (Thanks to @avera1988)
• Handles empty input genomes.
• Removed busco altogether. Had too many problems with hanging jobs and crashes/incomplete results.

v2.11.2

2.11.2

• Disabled any2fasta. Not relevant when only supporting fasta files is input anyway.
• Updated KEGG data from 2023-08-28 to 2024-08-13.
• Added --status functionality.
• Minor streamlining of code.
• Hard-coded eggnog decorate gff "yes" (#114)
• Made the panaroo rule and report section robust to a missing alignment file when the core is empty.

Full Changelog: v2.11.1...v2.11.2

v2.11.1

Full Changelog: v2.10.1...v2.11.1

2.11.1

• Speed up: Eggnog reuses the proteins called by the default annotation tool instead of redoing it itself with prodigal.
• Minor fixes.
• Enable antismash (still only works when using Conda and not Apptainer)
• Docker image did not contain bakta when annotator was set to prokka during containerization. Issue fixed within v2.10.1. Thanks to @flefler.
• Passthrough parameters notice removed.

v2.10.1

Full Changelog: v2.9.1...v2.10.1

2.10.1

• Breaking change: New Docker image (pinned eggnog)
• Variation in output files from Eggnog means that eggnog is now pinned to v2.1.12. Thanks to @michoug
• Quiet report output
• Minor fixes.

v2.9.1

Update: Please be aware that the first build (0) of this release had a wrong version string in the code. So if you see "v2.8.2", you might actually be running v2.9.1. From build 1, this is fixed.

Full Changelog: v2.8.2...v2.9.1

2.9.1

• Breaking change: new passthrough parameter system rolled out to most rules.
• Update cite value to reflect preprint doi https://doi.org/10.1101/2024.07.12.603264
• Add more tools to passthrough argument feature. And write documentation.
• Fixed an error that meant that panaroo was using the Prokka annotation (.gff) regardless of the annotator being set with --config annotator=[bakta|prokka].
• Fixed an error that meant that both Bakta and Prokka would run even though the user had selected one with --config annotator=[bakta|prokka]. Thanks to @michoug
• Minor fixes.

v2.8.2

What's Changed

• Update README.md by @wwood in #102

New Contributors

• @wwood made their first contribution in #102

Full Changelog: v2.8.1...v2.8.2

2.8.2

• Add --cite parameter to executable.
• New more differentiated logo for cli.
• Prints report sections in the end of the dynamic report pipeline.
• Explicit option to run prokka in archaea mode.
• config setting prokka_rfam is false by default.
• Brought Panaroo options out into config.
• Docker image follows minor version only. So all subsequent patches will use the same Docker image for Apptainer.
• New passthrough parameter system where parameters and arguments are automatically unpacked for each rule. Generalized implementation.
• Minor fixes.

v2.8.1 "Formerly known as Assemblycomparator2"

Full Changelog: v2.7.1...v2.8.1

2.8.1

• Breaking change: Changed named from Assemblycomparator2 to CompareM2.
• Compressed test files.
• Updated header text.
• Bring back the ass.
• Add --no-check-certificate to wget downloads.
• Added missing localrules for download rules.
• In profiles, decrease latency and add rerun-incomplete: true.
• Increase memory requirement for Bakta.
• Use dbcan_build to install that database.
• Disable antismash until issue is resolved.
• Updated the busco report section so it accepts the .faa file that was added in v2.7.1.
• Add tmpdir to eggnog.
• Compute md5sum of input genome in rule copy.
• Minor fixes.

v2.7.1

Full Changelog: v2.6.2...v2.7.1

2.7.1

• Breaking change: File hierarchy now follows what is recommended in the snakemake documentation. Rules are now in individual files.
• Breaking change: profiles/ moved to profile/ (sorry). And local profiles are now named "default".
• Busco runs in protein mode, reusing .faa from prokka (or bakta - see further down). Should result in speedup.
• Added Panaroo, removed Roary.
• For dbcan, only the substrates are shown in the dynamic report.
• Gtdb updated to release 220.0
• Add bakta.
• User can specify whether to use prokka or bakta to create annotation that is used for dbcan, interproscan diamond_kegg, busco. This can be set using --config annotator=bakta or by changing the permanent parameter in config/config.yaml.
• Add eggnog
• rename benchmark files from individual->Sample
• Add antismash. Uses .gbk from prokka.
• report_subpipeline renamed to dynamic_report
• Dynamic report is now run by the ./asscom2 binary instead of using onsuccess/onerror.
• Minor fixes.
• Software versions and database versions are written to hidden files within output directories.
• Added dynamic parameters to prokka and iqtree to the config file.
• Added support for a "fofn" which is a file of file names. In the tseemann style, it defines which input genomes to process.
• Use KEGG KO from eggnog in kegg_pathway. If this doesn't work well I'll consider re-implementing kofam_scan which was removed long time back. Now a_class and b_class are "class" and "group".
• Implemented a way to set the output directory which now defaults to the old static "results_ac2".
• Implemented TreeCluster that on the 4.5% and 10% basis defines clusters on the mashtree distances so the user can easily get an impression on the relative differences between samples.
• Fix an error that makes snp-dists results not show up in the report. (Thanks to @AstaLaugesen)
• Added documentation over at https://assemblycomparator2.readthedocs.io/en/latest/

v2.6.2

Full Changelog: v2.6.1...v2.6.2

2.6.2

• Fix wrong path for dbcan results (not yet implemented in report)
• Downgrade diamond 2.1.8 due to segfault in newest version (2.1.9) bbuchfink/diamond#785