v1.3.4

What's Changed

• Add update of documentation when making a release to README. by @njohner in #126
• Improve error handling for missing input genomes and reference databases. by @njohner in #130
• Add option to highlight certain leaves in custom plots. by @njohner in #131
• Add contig accession and range to genomic regions in plot_region. by @njohner in #134
• Display Venn diagram as Edwards for 6 genomes by @njohner in #135
• Add contig card to locusx view. by @njohner in #136
• Optimize order of regions in plot_region. by @njohner in #137
• Improve region edge representations in plot_region. by @njohner in #138
• Add contig table to genome overview (extract_contig view). by @njohner in #139
• Clean-up css files. by @njohner in #140
• Support for AMRFinder version 4 by @njohner in #141
• Fix reference database pipeline by @njohner in #142

Full Changelog: v1.3.3...v1.3.4

v1.3.3

What's Changed

• Update conda environments by @njohner in #121
• Add missing assets when running webapp with nginx and gunicorn. by @njohner in #122
• Fix kegg forms by @njohner in #123
• Update README with up to date installation information. by @njohner in #124

Full Changelog: v1.3.2...v1.3.3

v1.3.2

What's Changed

• Fix annotation pipeline for nextflow version > 24.03. by @njohner in #120

Full Changelog: v1.3.1...v1.3.2

v1.3.1

What's Changed

• Fix amrfinder database update for Linux. by @njohner in #113
• Fix conda checkm environment. by @njohner in #114
• Update containers for new zDB release v 1.3.0 by @njohner in #112
• Fix displaying zDB workflow images in sphinx documentation. by @njohner in #115
• Fix binding of folders when running with singularity. by @njohner in #116
• Update changelog to prepare release 1.3.1. by @njohner in #118

Full Changelog: v1.3.0...v1.3.1

Release v1.3.0: This release is broken, use 1.3.1

What's Changed

• Add script to compute rendering times of various views. by @njohner in #51
• Update and speed-up base DB setup script. by @njohner in #53
• Introduce comparison type specific mixins by @njohner in #49
• Add reference DB and software versions to database. by @njohner in #54
• Add virulence factor annotations. by @njohner in #56
• Various small bug fixes by @njohner in #57
• Add all the standard views for the virulence factors by @njohner in #58
• Webapp bug fixes and view improvements. by @njohner in #59
• Port remaining analysis views to class-based and introduce analysis metadata classes by @njohner in #60
• Cleanup html templates by @njohner in #61
• Small bug fixes for comparison index and hit extraction views. by @njohner in #63
• Fix blast view by @njohner in #64
• Add GWAS analyses using Scoary2 by @njohner in #62
• Fix blast against the VFDB. by @njohner in #65
• Bug fixes and more error handling in various views. by @njohner in #66
• Add specific form for GWAS analysis. by @njohner in #67
• Add phylogenetic representation of GWAS results by @njohner in #68
• Update annotation pipeline tests for VFs. by @njohner in #69
• Improve some results descriptions and cosmetic changes by @njohner in #70
• Feature/blast genomic region by @bkm in #52
• Add VFs to locus and orthogroup views. by @njohner in #71
• Speedup VF query by @njohner in #72
• Add AMRs and VFs to search index. by @njohner in #73
• Fix icons in comparison index views. by @njohner in #76
• Filter VF hits by SeqID and coverage and keep one hit per locus. by @njohner in #77
• Consistently use metadata objects in various views. by @njohner in #75
• Add view to produce custom plots (phylogenetic trees and table). by @njohner in #78
• Add command line variables for filtering VFs to bin/zdb. by @njohner in #79
• Fix home view for DBs with missing optional annotations. by @njohner in #80
• Fix bug in ValueColoredColumn. by @njohner in #81
• Allow defining groups of genomes in input file. by @njohner in #82
• Display form validation errors next to the corresponding fields. by @njohner in #83
• Handle groups in hit extraction view. by @njohner in #84
• Handle groups when selecting genomes wherever pertinent. by @njohner in #85
• Add views to add, delete, and display groups. by @njohner in #86
• Fix webapp conda environment for macOS. by @njohner in #87
• Control data exports from tables by making rows selectable. by @njohner in #88
• Add buttons to download protein and DNA sequences in homologs tables. by @njohner in #89
• Improve table layouts for venn and contigs views. by @njohner in #90
• Add button to draw custom phylogeny from selection of entries in various tables. by @njohner in #92
• Correctly handle group_0 in EntryIdParser. by @njohner in #93
• Fix various views for cases where there are no gene annotations. by @njohner in #99
• Fix typo in accumulation rarefaction plot metadata. by @njohner in #100
• Fix Scoary-2 integration. by @njohner in #101
• Fix product representation in GWAS view for orthogroups. by @njohner in #102
• Integrate link to paper blast in the locus overview. by @njohner in #103
• Add button to blast protein sequence in the locus overview. by @njohner in #104
• Fix Pfam identifiers by @njohner in #105
• Execute tblastn search against the fna (contigs) database. by @njohner in #106
• Update scoary2 reference and add paperBLAST to list of references by @njohner in #107
• Fix filtering of COGs in annotation pipeline. by @njohner in #108
• Update zDB documentation by @njohner in #110
• Fix displying workflows in README. by @njohner in #111

Full Changelog: v1.2.2...v1.3.0

Fixed issue with conda install

Increased version number to avoid issue where the build number was not taken into account by conda.

checkm fix

• updated checkm-genome

Use mamba

• use mamba to create envs

Conda bugfixes

v1.1.1

Moving tag to the latest commit

v1.1.0

Bugfixes and resume in db setup script