v0.7.4

What's Changed

• v0.7.4: code improvements by @matinnuhamunada in #277
• Improvement on metabase functionalities
• Use automlst wrapper from NBCHub
• Bug fixes: error in BiG-SCAPE summary due to region_id with BGC in it
• New feature: antiSMASH will scan for existing JSON and reuse it if possible, making the version update faster

Full Changelog: v0.7.3...v0.7.4

v0.7.3

What's Changed

• Metabase improvement by @matinnuhamunada in #276
• Exclude unused dbt models based on user provided configuration
• Synchronisation with bgcflow_dbt-duckdb v0.2.1 and bgcflow sync feature from bgcflow_wrapper v0.3.0

Full Changelog: v0.7.2...v0.7.3

v0.7.2

What's Changed

• Dev 0.7.2 by @matinnuhamunada in #274
• Improve reports structure and style
• Enable report to track dependency version from metadata
• Give flexibility to accept .fna, .fasta, or .fa for input
• Example config are now meant to be copied instead just a symlink
• Auto generate admin account of metabase on the first run
• CBlaster DB was generated from processed genbank instead of the raw prokka file

Full Changelog: v0.7.1...v0.7.2

v0.7.1

What's Changed

• Dev 0.7.1 by @matinnuhamunada in #258

• This release handles reproducibility problems and other bugs:

  • Handle large sample sizes by changing internal script input to text parsing instead of CLI arguments
  • Dependency fixes
  • Ignore invalid rules/pipelines instead of returning errors
  • Update links to external GTDB resources and handle version formatting
  • Move dependency version metadata to the processed folder
  • Improve quick start guide
  • Better test implementation: now testing conda environments using micromamba
  • Improve ARTS dependency
  • make sure all input exist before building database

Full Changelog: v0.7.0-alpha...v0.7.1

v0.7.0

This pre-release upgrade BGCFlow to use antiSMASH 7.0.0 and GTDB release 214.
Some other dependencies are not yet stable, hence a pre-release.

What's Changed

• Dev 0.7.0 by @matinnuhamunada in #254

• feat: upgrade to antismash 7

• feat: upgrade gtdbtk and gtdb to release 214

• chore: move default logs location

• chore: make an alias for rules/pipelines and name/pep

• fix: grab ARTS from release instead of git clone

• fix: correct ARTS setup

• feat: upgrade bigslice for compatibility with antiSMASH7

• test: update test for 0.7.0

• fix: enable ani_screen in gtdbtk

• fix: correct gtdb release versioning

• chore: set ani_screen off as default for gtdbtk

• docs: add quickstart video

• feat: upgrade extraction from mmseqs2 and clinker

• feat: process mmseqs2 cog feature

• fix: handle non standard BGC genbanks

• feat: enable to switch between antismash 7 and 6

• docs: mention about the WIKI

Full Changelog: v0.6.4...v0.7.0-alpha

v0.6.4

What's Changed

• handle missing custom gtdb taxonomy index by @matinnuhamunada in #250

Full Changelog: v0.6.3...v0.6.4

BGCFlow v0.6.3

What's Changed

• Dev 0.6.3 - Citation Update by @matinnuhamunada in #248
• Resolve vulnerability issues

Full Changelog: v0.6.2...v0.6.3

BGCFlow v0.6.2 patch release

This is a small patch that updates the quick start guide documentation in the README file.

What's Changed

• Dev 0.6.2 - Update README by @matinnuhamunada in #246

Full Changelog: v0.6.1...v0.6.2

BGCFlow v0.6.1 release

This is the release for BGCFlow initial submission to bioRxiv

What's Changed

Release 0.6.1 PR by @matinnuhamunada in #226

• [BREAKING CHANGE] Rollback setting temporary files for prokka output, this may trigger re-runs when updating from an older version of BGCFlow
• Fix GTDB API update bugs
• Log change of shortened accessions by antiSMASH can now be accessed in the processed directory
• Improvement in sub workflows
• Handle errors introduced by overlapping CDS among two or more regions
• Update pytorch dependencies for deepTF
• Includes CARD metadata from GTDB
• Handle empty results when MASH best k cluster cannot be determined
• Add summary annotation and CDS table from prokka
• Improvement of Jupyter Notebooks report template
• [IMPORTANT] Correct ARTS parameter to search for DUF and known resistance models
• [IMPORTANT] Use mix parameter for bigscape in BGC comparison
• New feature added: BGC comparison with mmseqs2 and minimap
• Use graphviz sfdp layout to process large network
• Handle unusual locus tag location with characters and joints
• Upgrade automlst to patch 0.1.1 for multiprocessing
• [BREAKING CHANGE] Remove obsolette rules
• Add figure statistics to roary report
• Upgrade metabase and database-related functions
• Export all csv to parquet as warehouse
• Add instruction to transfer SQL table relationship to metabase

Full Changelog: v0.6.0-alpha...v0.6.1

BGCFlow v0.6.0 pre-release

What's Changed

• Updates and new feature: BGC oriented sub-workflow by @matinnuhamunada in #215
• Update BiG-SCAPE (1.1.5) to use MIBIG 3.1
• Report notebook updates for rule: arts, cblaster, checkm, roary, and eggnog
• Introduce unit test for rules. Currently these are automatically generated from Snakemake, and only cover rules which can be run without specific conda environment
• antismash rule now generate a bgc table overview
• BGC oriented sub-workflow enable users to run: interproscan, clinker, bigscape, and bigslice. See .examples/lanthipeptide after running .examples/lactobacillus_delbrueckii. We have not tested this workflow to run multiple projects. This can be run with BGCFlow wrapper v0.2.2 :

bgcflow run --snakefile workflow/BGC

• Experimental docker container hosted in: "docker://matinnu/bgcflow:latest. This are not fully working yet and the size is huge.
• Introduce a subworkflow to run Metabase server. This can be run with BGCFlow wrapper v0.2.2 :

bgcflow --snakefile workflow/Metabase

• Bugs fix and integration with BGCFlow DBT-DuckDB pipeline

Full Changelog: v0.5.2-alpha...v0.6.0-alpha