Recent Releases of comparem2
comparem2 - v2.15.1
Full Changelog: https://github.com/cmkobel/CompareM2/compare/v2.14.1...v2.15.1
2.15.1
- Breaking change: Adding new conda environment to docker image containing the ncbi datasets cli tool.
- Add option to add ncbi analysis as comparison to local genomes using comparem2 --config add_ncbi=<accession>
- Changed the way --status works, so now it computes the summary ahead of time. #122
- Fixed an error where some sample basis jobs would rerun when other samples were added or removed.
- Added more in-depth documentation on the --until parameter
- Set Bakta as the default annotator (previously prokka, which is now deprecated)
- Report graphics are now exported as pdf (vector) into the results directory.
- Fixed bug regarding the snp-dists section in the report.
- Python
Published by cmkobel 6 months ago
comparem2 - v2.14.1
2.14.1 - Breaking change: New Docker image. - Added gapseq, rules "gapseqfind" and "gapseqfill" are done and ready. - Updated gtdbtk to release 226. - Minor fixes.
Full Changelog: https://github.com/cmkobel/CompareM2/compare/v2.13.1...v2.14.1
- Python
Published by cmkobel 8 months ago
comparem2 - v2.13.1
Full Changelog: https://github.com/cmkobel/CompareM2/compare/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.
- Python
Published by cmkobel about 1 year ago
comparem2 - v2.12.1
Full Changelog: https://github.com/cmkobel/CompareM2/compare/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.
- Python
Published by cmkobel about 1 year ago
comparem2 - 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: https://github.com/cmkobel/CompareM2/compare/v2.11.1...v2.11.2
- Python
Published by cmkobel about 1 year ago
comparem2 - v2.11.1
Full Changelog: https://github.com/cmkobel/CompareM2/compare/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.
- Python
Published by cmkobel over 1 year ago
comparem2 - v2.10.1
Full Changelog: https://github.com/cmkobel/CompareM2/compare/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.
- Python
Published by cmkobel over 1 year ago
comparem2 - 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: https://github.com/cmkobel/CompareM2/compare/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.
- Python
Published by cmkobel over 1 year ago
comparem2 - v2.8.2
What's Changed
- Update README.md by @wwood in https://github.com/cmkobel/CompareM2/pull/102
New Contributors
- @wwood made their first contribution in https://github.com/cmkobel/CompareM2/pull/102
Full Changelog: https://github.com/cmkobel/CompareM2/compare/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.
- Python
Published by cmkobel over 1 year ago
comparem2 - v2.8.1 "Formerly known as Assemblycomparator2"
Full Changelog: https://github.com/cmkobel/CompareM2/compare/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.
- Python
Published by cmkobel over 1 year ago
comparem2 - v2.7.1
Full Changelog: https://github.com/cmkobel/assemblycomparator2/compare/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 diamondkegg, 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.
- reportsubpipeline renamed to dynamicreport
- 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 keggpathway. If this doesn't work well I'll consider re-implementing kofamscan which was removed long time back. Now aclass and bclass are "class" and "group".
- Implemented a way to set the output directory which now defaults to the old static "resultsac2".
- 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/
- Python
Published by cmkobel over 1 year ago
comparem2 - v2.6.2
Full Changelog: https://github.com/cmkobel/assemblycomparator2/compare/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) https://github.com/bbuchfink/diamond/issues/785
- Python
Published by cmkobel almost 2 years ago
comparem2 - v2.6.1
Full Changelog: https://github.com/cmkobel/assemblycomparator2/compare/v2.5.18...v2.6.1
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.
- Python
Published by cmkobel almost 2 years ago
comparem2 - v2.5.18
Full Changelog: https://github.com/cmkobel/assemblycomparator2/compare/v2.5.17...v2.5.18
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/ac2-test-battery)
- Python
Published by cmkobel about 2 years ago
comparem2 - v2.5.17
Full Changelog: https://github.com/cmkobel/assemblycomparator2/compare/v2.5.16...v2.5.17
- 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.
- Python
Published by cmkobel about 2 years ago
comparem2 - v2.5.16
Full Changelog: https://github.com/cmkobel/assemblycomparator2/compare/v2.5.15...v2.5.16
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.
- Python
Published by cmkobel about 2 years ago
comparem2 - v2.5.12
Full Changelog: https://github.com/cmkobel/assemblycomparator2/compare/v2.5.11...v2.5.12
- Added motulizer.
Had to skip v2.5.11 as I forgot the motulizer.yaml file in that one which means that the dockerfile was not viable. This is fixed here.
- Python
Published by cmkobel over 2 years ago
comparem2 - v2.5.0
Changelog since last "release".
(2.5.0) - Apptainer support. New profiles for apptainer or conda use. - Abricate supported in report (ncbi, card, plasmidfinder, vfdb). - Add updated demo with Strachan Campylobacter
(2.4.1) - Adjusting the new report and fix minor bugs
(2.4.0) - New report based on child sections
Full Changelog: https://github.com/cmkobel/assemblycomparator2/compare/v2.3.0...v2.5.0
- Python
Published by cmkobel over 2 years ago
comparem2 - v2.3.0
New features: - GC - GTDB-tk - new report subpipeline - Not using drmaa - Not supporting singularity (but the dockerfiles are still pointed at) - Ready for implementing differential resources for varying number of input assemblies
Only minor bugs to fix
- Python
Published by cmkobel over 3 years ago
comparem2 - assemblycomparator2 is ready for rolling!
This version supports a local setup, but also a slurm-singularity based HPC setup. The report works as well. I will think about generating the report as a checkpoint rule instead though.
- Python
Published by cmkobel over 4 years ago
comparem2 - v2.0.0 alpha release
Most things work. But some testing - especially with singularity - is still needed.
- Python
Published by cmkobel almost 5 years ago