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/