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changelog.txt
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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.
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.
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.
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.
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.
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.
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.
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.
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 ./comparem2 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_comparem2".
- 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://comparem2.readthedocs.io/en/latest/
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) https://github.com/bbuchfink/diamond/issues/785
2.6.1
- Remove Kraken2, hence new minor version. Kraken2 really only makes sense on reads.
- Roary as a checkpoint, to only continue with iqtree, fasttree and snp-dists if the core genome is non-empty.
- conda yaml for wget. TODO, carry over to dbcan download as well.
2.5.18
- Support for weird characters in input files. #31
- Support for adding input files from other directories. #58
- Minor bugfixes. #77
- Test battery is being developed. (https://github.com/cmkobel/comparem2-test-battery)
2.5.17
- Forced recompilation of docker image did not fix issue #74. This patch has equivalent .yaml-files to version 2.5.14, which means that the old (working) docker image will be compatible.
2.5.16
- Indirect bug because of an uncaught docker error. Forced recompilation of the image should fix that.
- Propagation of version string to easy version bumping.
2.5.15
- Limited snakemake version because of breaking dependency changes herein.
2.5.14
- problems with dockerfile fixed
2.5.13
- Bugfix: Wrong number of bootstraps for quicktree
2.5.12
- motulizer.yaml was missing.
2.5.11
- Added support for motulizer and motupan. Yet lacking in report and awaits further integration.
2.5.10
- comparem2 now supports iqtree with bootstrapping. Runs on the core genome produced by roary. Yet to be included in the report.
2.5.9
- Fixed an error where checkm2 would fail setting the download location internally when running comparem2 using the apptainer/docker container. https://github.com/chklovski/CheckM2/issues/73
2.5.8
- Fixed an error where a different version of the docker image would be pulled for the report subpipeline
2.5.7
- Fixed an error where a conda environment would not be activated when using the apptainer profile for slurm.
2.5.6
- New ./comparem2 "binary" to replace the old alias. This "binary" comes with default environment variables.
2.5.5
- Use $ASSCOM_DATABASES to define where the databases are placed.
- Docker images have a versioning system so an incompatible image can't be used.
2.5.4
- Using the mashtree order in plots in the report. Using alphabetical order redundantly in case mashtree hasn't run (sucessfully). Minor adjustments to other plots. TODO: midpoint root tree somehow and order all tables in the report as well.
2.5.3
- Using snakemake's --containerize to automatically generate images which are then synced to dockerhub as cmkobel/comparem2. Support for hpc queues isn't yet tested.
2.5.2
- dbcan, including download
- interproscan
- both dbcan and interproscan are yet to be integrated in the report
2.5.0
- Apptainer support. New profiles for apptainer or conda use.
2.4.1
- Adjusting the new report and fix minor bugs
2.4.0
- New report based on child sections
2.3.0
- Disabled pathway enrichment as conda failed
- Implemented GTDB-tk
- Having problems with Prokka
2.2.0
- Sample pathway enrichment analysis with clusterProfiler which is integrated into the report.
- Considering going away from singularity: Too much maintenance and too little return when it has to work with conda anyway. I haven't completely decided yet, but leaning strongly.
2.1.1
- Simple GC statistics added to output and report
2.1.0
- Bug and stability issues fixed
2.0.0
- Completely new system based on snakemake using both slurm and singularity