v0.8.3

What's Changed

This release adds enhanced iTOL integration and documentation Updates @matinnuhamunada in #337

• feat: Export tree and annotation tables for iTOL
• docs: update DAG and tables to include GECCO
• chore: add misc notebook to recreate the beautified DAG

Full Changelog: v0.8.2...v0.8.3

v0.8.2

What's Changed

This release incudes additional feature and report improvements, especially visualization of results.

Feats:

• feat: fine-grained antiSMASH database to improve resource reusability by @matinnuhamunada in #332
• feat: add visualization of COG category across pangenes by @matinnuhamunada in #333
• feat: NEW predict BGCs with GECCO by @matinnuhamunada in #334
• feat: NEW explore and analyze natural sequence variations within the Open Reading Frames (ORFs) of alleles of core genes in a species' pan-genome using Alleleome 0.1.0 by @matinnuhamunada in #326

Notebooks & chores

• chore: notebooks Improvements by @matinnuhamunada in #329
• notebooks: fix small errors by @matinnuhamunada in #331
• notebooks: notebooks update by @matinnuhamunada in #335
• notebooks: add gecco report and improve tree visualization by @matinnuhamunada in #336

Full Changelog: v0.8.1...v0.8.2

v0.8.1

What's Changed

v0.8.1 by @matinnuhamunada in #309

This release includes several bug fixes, feature enhancements, and test updates.

• Bug Fixes
  • Fixed Roary report issue in Roary (#310)
  • Fixed BiG-SCAPE notebook
  • Fixed peppy issue in bgcflow build report (#313)
  • Created symlink to assets in the processed docs folder
  • Corrected Roary asset path for notebook report
  • Added new wildcard constants for genbank input to lsabgc and ppangolin
  • Corrected wildcard constants and rule dependencies in subworkflow
  • Corrected custom input path
  • Corrected BGC subworkflow dependencies and input format
  • Corrected broken MIBIG link
  • Used custom database path for checking antismash 6 pre-requisites
  • Pinned peppy version due to backward-incompatibility in v40
• Features
  • Enabled Metabot to enable OpenAI interaction in Metabase
• Tests
  • Added GitHub action for sub-workflows
  • Updated dry-run test configurations
  • Added BGC project example
  • Added input data for BGC subworkflow test
  • Updated snakemake action
• Chores
  • Removed unused print statement

Patch 0.8.1-1 by @matinnuhamunada in #314

This patch includes several bug fixes, feature enhancements, and test updates primarily focused on improving the BGC sub-workflow visualization feature.

• Bug Fixes
  • Applied wildcard constraints for software version and fixed input path
  • Corrected clinker coloring scheme
  • Handled missing locus tag in MIBIG entries
• Features
  • Added color and annotation to clinker using antismash
• Tests
  • Used alternative repo for snakemake action
• Chores
  • Set intermediate annotation to temp

Patch 0.8.1-2 by @matinnuhamunada in #317

This patch includes several bug fixes and chores, primarily focused on updating notebooks and scikit parameters.

• Bug Fixes
  • Updated to scikit-learn 1.4.0 to address deprecated parameters in mash and fastani notebooks
• Chores
  • Updated actions
  • Reset to alternative snakemake action
  • Changed tempdir for eggnog

Patch 0.8.1-3 by @matinnuhamunada in #318

This patch includes several bug fixes and chores, primarily focused on adding missing elements and correcting typos.

• Bug Fixes
  • Included df_mibig_bgcs in the final output of ppanggolin
  • Included missing rule dependencies
• Chores
  • Corrected typo in messages

Full Changelog: v0.8.0...v0.8.1

v0.8.0

What's Changed

• V0.8.0: Enable genbank inputs by @matinnuhamunada in #306

Full Changelog: v0.7.9...v0.8.0

v0.7.9

What's Changed

New features by @matinnuhamunada in #300

• feat: Add getphylo to BGC subworkflow for making BGC tree
• feat: Build pangenome graph and region of genome plasticity analysis with ppanggolin

Fix patches - 0.7.9-1 by @matinnuhamunada in #304:

• notebook: add instruction for BiG-SCAPE cytoscape network loading
• fix: handle BiG-FAM model without taxonomic assignment
• fix: Support for antismash 6 meme version
• fix: replace set with pandas unique as it is not consistent
• fix: resolve relative paths for working remotely or in a cluster
• fix: handle BGC subworkflow bugs

Full Changelog: v0.7.8...v0.7.9

v0.7.8

What's Changed

New features

• feat: add lsabgc ready & autoanalyze subworkflow for in depth evolutionary and popgen statistics by @matinnuhamunada in #289
• feat: Enable GTDB API offline mode. This is useful when GTDB API is down or when having a huge query by @matinnuhamunada in #295

Fixes & others

• fix: resolve BlockingIOError in alpine #282 (reply in thread)
• fix: handle Roary output error
• fix: antismash 6 environments installation
• docs: add funding notes
• fix: evaluate gtdbtk rule. If no genomes are eligible, then generate empty table
• fix: BGC sub workflow

Full Changelog: v0.7.7...v0.7.8

v0.7.7

What's Changed

• Dev 0.7.7 - Fixes by @matinnuhamunada in #291
• bigslice_query: Normalization of the feature in was introduced in this commit: medema-group/bigslice@8be91ac, which causes query against the current BiG-FAM db (built using BiG-SLICE v1.0.0) always hit the same GCFs, whatever the input is. A fork of the BiG-SLICE is made with the option to turn off the normalization https://github.com/NBChub/bigslice
• bigslice_cluster: The normalization changes the scale of the threshold, from 900 to 0.4 as mentioned in #263
• arts: handle error when no resistance model is hit
• database: pin duckdb version
• notebook: FASTANI matrix need correction as the pairwise hit of own genomes is null, it should be 100
• update on notebook visualizations

Full Changelog: v0.7.6-1...v0.7.7

v0.7.6-1

This patch fixes minor issues found in the previous release:

• Error in BiG-SLICE query shell
• Error in building ARTS environment due to matplotlib and numpy installed separately (one with conda and the other with pip)
• Error in building R notebook environment due to update in gggenomes.

Full Changelog: v0.7.6...v0.7.6-1

v0.7.6

What's Changed

This release updates the notebook report for BGCFlow:

• Dev 0.7.6 - Notebook updates by @matinnuhamunada in #285
• eggnog: show COG distribution with heatmap
• deepTF: annotate hits with annotation from faa headers
• BiG-SCAPE: generate graphml file for cytoscape visualization (top hit to KnownClusterBlast included)
• ARTS: extract information from the 4 tables (dup, phylogeny, bgc, and known model)
• BiG-FAM: annotate taxonomy of BiG-FAM model hits
• CBLASTER: update instruction
• fix: update GTDB API test
• dependencies: include Java and pin python to 3.11 in getting started

Full Changelog: v0.7.5...v0.7.6

v0.7.5

What's Changed

• Dev 0.7.5 by @matinnuhamunada in #281

• Fix error when re-using antiSMASH JSON
• Relax Roary cluster size limit
• Fix deepTF output

Full Changelog: v0.7.4...v0.7.5