bgcflow - v1.1.2

What's Changed

This is version only works with bgcflow_wrapper version < 0.5.0 * fix: transition from conda defaults by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/365 * fix: correct dfgenepresenceabsencebinary.csv location by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/365

Full Changelog: https://github.com/NBChub/bgcflow/compare/v1.1.1...v1.1.2

- Python
Published by matinnuhamunada over 1 year ago

bgcflow - v1.1.1

Release Notes

Version v1.1.1

• This release update GTDB to version 220 and enables the usage of environment variable to change antiSMASH mode (e.g. fungi).

What's Changed

• fix: MIBiG and BiG-SCAPE fixes by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/356
• feat: update gtdbtk to v220 by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/362

Full Changelog: https://github.com/NBChub/bgcflow/compare/v1.1.0...v1.1.1

- Python
Published by matinnuhamunada over 1 year ago

bgcflow - 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: https://github.com/NBChub/bgcflow/compare/v1.0.0...v1.1.0

- Python
Published by matinnuhamunada over 1 year ago

bgcflow - v1.0.0

What's Changed

BGCFlow version 1.0.0 by release by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.9.3...v1.0.0

- Python
Published by matinnuhamunada over 1 year ago

bgcflow - v0.9.3

What's Changed

This release include small bug fixes by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.9.2...v0.9.3

- Python
Published by matinnuhamunada almost 2 years ago

bgcflow - 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 https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.9.1...v0.9.2

- Python
Published by matinnuhamunada almost 2 years ago

bgcflow - 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 https://github.com/NBChub/bgcflow/pull/340

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.9.0...v0.9.1

- Python
Published by matinnuhamunada almost 2 years ago

bgcflow - v0.9.0

What's Changed

New Features by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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 inputfile and gbkpath 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 https://github.com/NBChub/bgcflow/pull/327

New Contributors

• @JackSun1997 made their first contribution in https://github.com/NBChub/bgcflow/pull/327

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.8.3.2...v0.9.0

- Python
Published by matinnuhamunada almost 2 years ago

bgcflow - v0.8.3.2

What's Changed

This release adds enhanced iTOL integration and documentation Updates @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.8.2...v0.8.3.2

- Python
Published by matinnuhamunada about 2 years ago

bgcflow - v0.8.3.1

What's Changed

This release adds enhanced iTOL integration and documentation Updates @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.8.2...v0.8.3.1

- Python
Published by matinnuhamunada about 2 years ago

bgcflow - v0.8.3

What's Changed

This release adds enhanced iTOL integration and documentation Updates @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.8.2...v0.8.3

- Python
Published by matinnuhamunada about 2 years ago

bgcflow - 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 https://github.com/NBChub/bgcflow/pull/332
• feat: add visualization of COG category across pangenes by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/333
• feat: NEW predict BGCs with GECCO by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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 https://github.com/NBChub/bgcflow/pull/326

Notebooks & chores

• chore: notebooks Improvements by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/329
• notebooks: fix small errors by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/331
• notebooks: notebooks update by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/335
• notebooks: add gecco report and improve tree visualization by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/336

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.8.1...v0.8.2

- Python
Published by matinnuhamunada about 2 years ago

bgcflow - v0.8.1

What's Changed

v0.8.1 by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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 https://github.com/NBChub/bgcflow/pull/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 https://github.com/NBChub/bgcflow/pull/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 https://github.com/NBChub/bgcflow/pull/318

This patch includes several bug fixes and chores, primarily focused on adding missing elements and correcting typos. - Bug Fixes - Included dfmibigbgcs in the final output of ppanggolin - Included missing rule dependencies - Chores - Corrected typo in messages

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.8.0...v0.8.1

- Python
Published by matinnuhamunada about 2 years ago

bgcflow - v0.8.0

What's Changed

• V0.8.0: Enable genbank inputs by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/306

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.7.9...v0.8.0

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.7.9

What's Changed

New features by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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 https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.7.8...v0.7.9

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.7.8

What's Changed

New features

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

Fixes & others

• fix: resolve BlockingIOError in alpine https://github.com/NBChub/bgcflow/discussions/282#discussioncomment-7270753
• 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: https://github.com/NBChub/bgcflow/compare/v0.7.7...v0.7.8

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.7.7

What's Changed

• Dev 0.7.7 - Fixes by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/291
• bigslice_query: Normalization of the feature in was introduced in this commit: https://github.com/medema-group/bigslice/commit/8be91acf2637c5a3e81f38036dceecd596966a5b, 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 https://github.com/NBChub/bgcflow/issues/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: https://github.com/NBChub/bgcflow/compare/v0.7.6-1...v0.7.7

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - 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: https://github.com/NBChub/bgcflow/compare/v0.7.6...v0.7.6-1

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.7.6

What's Changed

This release updates the notebook report for BGCFlow: * Dev 0.7.6 - Notebook updates by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.7.5...v0.7.6

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.7.5

What's Changed

• Dev 0.7.5 by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/281
• Fix error when re-using antiSMASH JSON
• Relax Roary cluster size limit
• Fix deepTF output

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.7.4...v0.7.5

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.7.4

What's Changed

• v0.7.4: code improvements by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.7.3...v0.7.4

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.7.3

What's Changed

• Metabase improvement by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.7.2...v0.7.3

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.7.2

What's Changed

• Dev 0.7.2 by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.7.1...v0.7.2

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.7.1

What's Changed

• Dev 0.7.1 by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.7.0-alpha...v0.7.1

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - 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 https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.6.4...v0.7.0-alpha

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - v0.6.4

What's Changed

• handle missing custom gtdb taxonomy index by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/250

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.6.3...v0.6.4

- Python
Published by matinnuhamunada over 2 years ago

bgcflow - BGCFlow v0.6.3

What's Changed

• Dev 0.6.3 - Citation Update by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/248
• Resolve vulnerability issues

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.6.2...v0.6.3

- Python
Published by matinnuhamunada almost 3 years ago

bgcflow - 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 https://github.com/NBChub/bgcflow/pull/246

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.6.1...v0.6.2

- Python
Published by matinnuhamunada almost 3 years ago

bgcflow - 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 https://github.com/NBChub/bgcflow/pull/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: https://github.com/NBChub/bgcflow/compare/v0.6.0-alpha...v0.6.1

- Python
Published by matinnuhamunada almost 3 years ago

bgcflow - BGCFlow v0.6.0 pre-release

What's Changed

• Updates and new feature: BGC oriented sub-workflow by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/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 : bash 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 : bash bgcflow --snakefile workflow/Metabase
• Bugs fix and integration with BGCFlow DBT-DuckDB pipeline

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.5.2-alpha...v0.6.0-alpha

- Python
Published by matinnuhamunada about 3 years ago

bgcflow - v0.5.2-alpha

What's Changed

• fix: rollback bigslice to v1.1.1 by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/213

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.5.1-alpha...v0.5.2-alpha

- Python
Published by matinnuhamunada over 3 years ago

bgcflow - v0.5.1-alpha

What's Changed

• Patch 0.5.1 by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/207
• Fix GTDB API related issues https://github.com/NBChub/bgcflow/issues/202
• Database building via DBT and DuckDB: https://github.com/NBChub/bgcflow_dbt-duckdb
• ARTS2 processing: https://github.com/NBChub/arts_v3 https://github.com/NBChub/bgcflow/issues/158

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.5.0-alpha...v0.5.1-alpha

- Python
Published by matinnuhamunada over 3 years ago

bgcflow - v0.5.0-alpha

Feature Added

• Build diamond database for custom searches using CBlaster
• Enable overlapping sample ids by PEP integration
• Integrate BGCFlow with wrapper by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/198
• Generate notebook reports compatible with MKDocs by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/200
• Automate description and citation from rules
• AntiSMASH update to 6.1.1
• GC calculation via SeqFu2
• Introduce more scatter-gather approaches in rule execution
• Introduce database generation via DBT and DuckDB

What's Changed

• Fix BiG-SCAPE and BiG-SLICE processing by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/174
• fix: pin diamond version for cblaster by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/178
• feat: add gtdbtk rule for taxonomy by @OmkarSaMo in https://github.com/NBChub/bgcflow/pull/172
• GTDB-tk fix and update to R207 by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/183
• feat: Add information from PATRIC database by @OmkarSaMo in https://github.com/NBChub/bgcflow/pull/191
• feat: BGCFlow v1.x feature roadmap by @matinnuhamunada in https://github.com/NBChub/bgcflow/pull/192

Full Changelog: https://github.com/NBChub/bgcflow/compare/v0.3.3-alpha...v0.5.0-alpha

- Python
Published by matinnuhamunada over 3 years ago

bgcflow - BGCflow v0.3.3

A pre-release demo during the 2022 KAIST visit to DTU workshop.

- Python
Published by matinnuhamunada over 3 years ago