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CHANGELOG.md

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Changelog

Versions are of the form MAJOR.MINOR.PATCH and this changelog tries to conform to Common Changelog

Unreleased

Fixed

Changed

  • Cite zDB paper on home page and about pages. (#147) (Niklaus Johner)

Added

  • Add command line parameter to set CSRF_TRUSTED_ORIGINS. (#145) (Niklaus Johner)

1.3.4 - 2024-11-06

Fixed

  • Fix annotation pipeline for new AMRFinder version 4. (#141) (Niklaus Johner)
  • Fix DB setup pipeline when using containers and an unmounted reference directory. (#142) (Niklaus Johner)

Changed

  • Display Venn diagram as Edwards for 6 genomes, as numbers were missing in the classic representation. (#135) (Niklaus Johner)
  • Add contig accession and range to genomic regions in plot_region. (#134) (Niklaus Johner)
  • Improve error handling for missing input genomes and reference databases. (#130) (Niklaus Johner)
  • Optimize order of regions in plot_region. (#137) (Niklaus Johner)
  • Improve region edge representations in plot_region. (#138) (Niklaus Johner)
  • Add contig table to genome overview (extract_contig view). (#139) (Niklaus Johner)
  • Clean-up css files. (#140) (Niklaus Johner)

Added

  • Add contig card to locusx view. (#136) (Niklaus Johner)
  • Add option to highlight certain leaves in custom plots. (#131) (Niklaus Johner)

1.3.3 - 2024-08-08

Fixed

  • Fix Kegg based comparative analysis form. (#123) (Niklaus Johner)
  • Add missing assets when running webapp with nginx and gunicorn. (#122) (Niklaus Johner)
  • Fix checkm conda environment. (#121) (Niklaus Johner)

1.3.2 - 2024-07-30

Fixed

  • Fix annotation pipeline for nextflow version > 24.03. (#120) (Niklaus Johner)

1.3.1 - 2024-07-19

Fixed

  • Fix binding of folders when running with singularity. (#116) (Niklaus Johner)
  • Fix checkM conda environment. (#114
  • Fix AMRFinderPlus database update for Linux. (#113
  • Fix AMRFinderPlus database update for Linux. (#113
  • Update containers zDB release v 1.3. (#112

1.3.0 - 2024-07-11 (broken release as containers are outdated)

Changed

  • Update the documentation. (#110) (Niklaus Johner)
  • Execute tblastn search against the fna (contigs) database. (#106
  • Handle groups when selecting genomes wherever pertinent. (#84 and #85) (Niklaus Johner)
  • Allow using groups to define phenotype in GWAS view. (#82) (Niklaus Johner)
  • Display form validation errors next to the corresponding fields. (#83) (Niklaus Johner)
  • Filter VF hits by SeqID and coverage and keep one hit per locus. (#77) (Niklaus Johner)
  • Improve layout for various views, making better use of available space. (#70) (Niklaus Johner)
  • Configure repository to publish the docs to readthedocs
  • Port nextflow pipelines to DSL2 language. (#26) (Niklaus Johner)
  • Add CHANGELOG file. (#25) (Niklaus Johner)
  • Imported metagenlab_lib code into zdb (#33) (Bastian Marquis)
  • Removed eutils module. (#47) (Niklaus Johner)
  • Show xaxis labels (as links) in heatmap view. (#59) (Niklaus Johner)
  • Remove unused html templates. (#61) (Niklaus Johner)

Added

  • Add button to blast protein sequence in the locus overview. (#104) (Niklaus Johner)
  • Integrate link to paper blast in the locus overview. (#103) (Niklaus Johner)
  • Add button to draw custom phylogeny from selection of entries in various tables. (#92) (Niklaus Johner)
  • Add buttons to download protein and DNA sequences in homologs tables. (#89) (Niklaus Johner)
  • Control data exports from tables by making rows selectable. (#88) (Niklaus Johner)
  • Add views to add, delete, and display groups. (#86) (Niklaus Johner)
  • Allow defining groups of genomes in input file. (#82) (Niklaus Johner)
  • Add view to produce custom plots (phylogenetic trees and table). (#78) (Niklaus Johner)
  • Add AMRs and VFs to search index. (#73) (Niklaus Johner)
  • Add VFs to locus and orthogroup views. (#71) (Niklaus Johner)
  • Add new statistics to home view. (#70) (Niklaus Johner)
  • Add GWAS views. The associations are calculated using Scoary2. (#62) (Niklaus Johner)
  • Add VF details view. (#58) (Niklaus Johner)
  • Add VF accumulation/rarefaction plot view. (#58) (Niklaus Johner)
  • Add VF heatmap view. (#58) (Niklaus Johner)
  • Add VF tabular comparison views. (#58) (Niklaus Johner)
  • Add VF Venn diagram view. (#58) (Niklaus Johner)
  • Add VF hit extraction view. (#58) (Niklaus Johner)
  • Add VF comparison index view and link it in the menu and home page. (#58) (Niklaus Johner)
  • Add VF entry list view. (#58) (Niklaus Johner)
  • Add virulence factor annotations. (#56) (Niklaus Johner)
  • Store reference DB and software versions in DB. (#54) (Niklaus Johner)
  • Add script to compute rendering times of various views. (#51) (Niklaus Johner)
  • Add possibility to dump HTML responses from webapp tests. (#50) (Niklaus Johner)
  • Add AMR accumulation/rarefaction plot view. (#46) (Niklaus Johner)
  • Add AMR heatmap view. (#45) (Niklaus Johner)
  • Add AMR details view. (#44) (Niklaus Johner)
  • Add AMR Venn diagram view. (#41) (Niklaus Johner)
  • Add AMR hit extraction view. (#38) (Niklaus Johner)
  • Add AMR entry list view. (#37) (Niklaus Johner)
  • Add AMR comparison index view and link it in the menu and home page. (#35) (Niklaus Johner)
  • Add AMR tabular comparison views. (#24, #31) (Niklaus Johner)
  • Add integration tests for pipelines and views. (#29) (Niklaus Johner)
  • Add unitesting for pipelines. (#26) (Niklaus Johner)
  • Add antimicrobial resistance annotations. (#23) (Niklaus Johner)
  • Add support for circular contigs in the genomic viewer. (#33) (Bastian Marquis)

Fixed

  • Fix filtering of COGs in annotation pipeline. (#108
  • Fix blast view for hits with identifier containing a version number. (#106
  • Fix PFAM identifiers missing leading 0. (#105) (Niklaus Johner)
  • Fix product representation in GWAS view for orthogroups. (#102) (Niklaus Johner)
  • Fix Scoary-2 integration. (#101) (Niklaus Johner)
  • Fix search_bar results view when all loci miss any gene annotation. (#99) (Niklaus Johner)
  • Fix locusx view error for loci with homologs without any gene annotation. (#99) (Niklaus Johner)
  • Fix extract_contigs view error for contigs without any gene annotation. (#99) (Niklaus Johner)
  • Correctly handle group_0 in EntryIdParser. (#93) (Niklaus Johner)
  • Fix webapp conda environment for macOS. (#87) (Niklaus Johner)
  • Fix displaying active tab in search results view. (#73) (Niklaus Johner)
  • Fix missing page title for kegg_mapp_ko view. (#66) (Niklaus Johner)
  • Handle empty result set in heatmap, venn and pan_genome views. (#66) (Niklaus Johner)
  • Fix tabular comparison views navigation tabs. (#30, #31) (Niklaus Johner)
  • Fix the representation of genes overflowing from a genomic region, that would appear shorter than they actually are. (#52) (Bastian Marquis)
  • Fix missing page title on error in blast view. (#64) (Niklaus Johner)

1.2.1 - 2023-10-16

Changed

  • Bump checkm-genome version to 1.2.2. (Trestan Pillonel)

1.2.0 - 2023-10-13

Changed

Fixed

  • Fix issue for genome file download (#16) (Trestan Pillonel)
  • Fix file extensions in annotation pipeline (#17) (Thomas Kozusnik)

1.1.1 - 2023-05-16

Fixed

  • Fixed several issues with conda environments. (Bastian Marquis and Trestan Pillonel)

1.1.0 - 2023-03-30

Added

1.0.8 - 2023-03-15

Added

  • Add support for docker and conda. (#13) (Bastian Marquis)

Fixed

  • Several bugfixes

1.0.5 - 2022-12-08

Added

  • Add --resume option to zdb run (#11) (Bastian Marquis)
  • Add name field to the input csv file.
  • Accept genbank files with other extensions in the pipeline.

1.0.4 - 2022-09-21

Fixed

  • Fix conda build (#10) (Bastian Marquis)

1.0.3 - 2022-06-07

Fixed

1.0.2 - 2022-05-10

Added

  • Add support for conda. (#9) (Bastian Marquis)

1.0.0 - 2022-04-01

Initial release.