v1.1.0

Release Notes

Version v1.1.0

• This update includes a new database feature and a new tool for antimicrobial resistance detection.
• When running bgcflow build database, it will include also an antiSMASH database schema on top of BGCFlow results. This antiSMASH database follows the antiSMASH DB version 4 schema, including 65 tables extracted from antiSMASH JSON files.
• The database is designed to be compatible with the upcoming ChatBGC RAG chatbot

What's Changed

• Feature: Added AMRFinderplus integration by @matinnuhamunada in PR #353
• Feature: Implemented the ability to build a local antiSMASH database using DuckDB by @matinnuhamunada in PR #354
• Feature: Introduced a custom script to run the BiG-SCAPE notebook with user-defined cutoffs
• Fix: Corrected the process of copying GTDB-Tk results to the processed folder

Full Changelog: v1.0.0...v1.1.0

v1.0.0

What's Changed

BGCFlow version 1.0.0 by release by @matinnuhamunada in #348

New Features

• Database Schema Update: Upgraded to bgcflow database schema 0.3.1.
• Custom Taxon Parameter: Enabled parameter to change taxon in antiSMASH.
• antiSMASH Parameters: Added new parameters for antiSMASH based on the antiSMASH database 4 paper.

Fixes

• BGC Downstream Preparation:
  • Updated the BGC genome preparation script to handle unusual input formats (for example, includes ":" in the metadata) which breaks BiG-SCAPE.
  • Changed input requirements and corrected issues to ensure all changes are properly registered.
  • Reincluded full antiSMASH genbanks for downstream processes.
  • Modified the get_antismash_inputs function to correctly retrieve region genbanks.
• lsabgc: Updated lsabgc to version 1.52
• CheckM: Pinned numpy to version 1.26.4 for compatibility with CheckM.
• Recognized Formats: Included .gbff as a recognized format.

Documentation

• Citation Update: Updated the citation information to the BGCFlow publication at NAR.

Tests

• Action Corrections:
  • Micromamba Version: Fixed the Micromamba version in tests.
  • Snakemake Version: Ensured tests use the Snakemake version from the wrapper.
  • NCBI Metadata: Updated the expected NCBI metadata for tests.
  • Build Test Updates: Dropped build tests for antiSMASH 6 and lsabgc.
  • Setuptools Compatibility: Pinned setuptools to versions below 70.0.0.

Full Changelog: v0.9.3...v1.0.0

v0.9.3

What's Changed

This release include small bug fixes by @matinnuhamunada in #345

• fix: when converting custom genbank file, handle case where strain information is not found from source qualifiers
• fix: handle missing BiG-SCAPE class in building Jupyter notebook report
• fix: add parameters setting to change MASH sketch size, but keep the default value (1000). This value will be evaluated in the next release if a higher value are required to have better resolution at differentiating sub-species

Full Changelog: v0.9.2...v0.9.3

v0.9.2

What's Changed

This release improves the functionality of using genbank file as the inputs.

• feat: handle mixed input file types (fna & gbk) in a project by @matinnuhamunada in #344
• feat: generate a prokka-like summary stats for custom genbank inputs
• fix: add temporary DAG requirement of GTDB json for automlst-wrapper, will use final taxonomy output table in the future
• fix: update bcbio-gff and biopython to handle broken gff parsing during gbk conversion
• fix: add fna as default extension value for projects
• chore: ignore tables in notebooks folder for parquet conversion
• chore: test update GTDB card result from the latest API release (v220)

Full Changelog: v0.9.1...v0.9.2

v0.9.1

What's Changed

This PR fix the issue of antiSMASH 7.1.0 installation by pinning the meme 4.11.2 and updates the required resources: comparippson/asdb/4.0, and pfam/35.0

• fix: update antiSMASH resources and requirements by @matinnuhamunada in #340

Full Changelog: v0.9.0...v0.9.1

v0.9.0

What's Changed

New Features by @matinnuhamunada in #339

• Upgrade antiSMASH to version 7.1.0 (42533e9)
• Upgrade BiG-SCAPE to version 1.1.9 (5cf8be8)
• Upgraded DuckDB and Metabase for enhanced database management and analytics (6bb8d07).
• Upgraded CheckM (dbe5c6c).
• Upgraded Seqfu2 (bf77b2b).
• Upgraded Clinker and Cblaster (d911b29, a1f6da0).
• Added a script to facilitate database uploads to Motherduck, improving the data integration process (29290e6).

Fixes

• Symlink Generation: Improved symlink generation for downstream biosynthetic gene cluster (BGC) preparation and sanitation processes (096a925).
• JSON Schema Compatibility: Addressed issues with incompatible JSON schema from older antiSMASH versions (d50f6a9).
• Project Example Update: Updated the example BGC project to be compatible with antiSMASH 7.1.0 (90b6d33).
• Input Handling: Enhanced handling of inputs when both input_file and gbk_path are specified in the configuration sample (a38fb1f).
• Empty Value Handling: Improved handling of empty values to prevent data errors (9750419).
• Log Path Correction: Corrected the log path for Patric downloads, ensuring accurate logging (ef70724).
• Clean strange character for Roary post-analysis by @JackSun1997 in #327

New Contributors

• @JackSun1997 made their first contribution in #327

Full Changelog: v0.8.3.2...v0.9.0

v0.8.3.2

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
• chore: bump version to v0.8.3.1
• fix: handle null values for tree visualization

Full Changelog: v0.8.2...v0.8.3.2

v0.8.3.1

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
• chore: bump version to v0.8.3.1

Full Changelog: v0.8.2...v0.8.3.1

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