v2.16.2

Full Changelog: v2.16.1...v2.16.2

2.16.2

• Fixed wrong database path for bakta and antismash

Known issues with this version:
- This version incorrectly states that it is version v2.16.1

v2.16.1

Full Changelog: v2.15.3...v2.16.1

2.16.1

• 2nd try: Fixed some versions in the conda environments (has little to no effect on the overall pipeline). All conda environments now solve in strict channel priority mode.
• Database downloads into a version-minor named directory inside environment variable $COMPAREM2_DATABASES
• Updated checkm2 database and pinned the conda env to the minimum version that supports this database.
• Updated eggnog to v2.1.13

v2.15.3

Full Changelog: v2.15.2...v2.15.3

2.15.3

• Reverted refactored workflow envs (.yaml) as the previous release (v2.15.2) was a patch and not a minor release.

v2.15.2

Full Changelog: v2.15.1...v2.15.2

2.15.2:

• New add_ncbi batch downloader with advanced caching.
• Fixed snakemake keep-incomplete to false.
• Fixed some versions in the conda environments (has little to no effect on the overall pipeline). All conda environments now solve in strict channel priority mode.
• Updated CI tests so they use strict channel priority.
• Added escaped parentheses to the --gram "?" setting in bakta as it otherwise triggers an error when running with docker/apptainer.

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⚠️ This release is linked to the wrong docker image, so it should not be used. Use v2.15.1 or the newest version instead. If you're not using apptainer, this is not an issue.

v2.15.1

Full Changelog: 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.

v2.14.1

2.14.1

• Breaking change: New Docker image.
• Added gapseq, rules "gapseq_find" and "gapseq_fill" are done and ready.
• Updated gtdbtk to release 226.
• Minor fixes.

Full Changelog: v2.13.1...v2.14.1

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.