Code

Updates and BGC Feature#215

Code

Merged

matinnuhamunada merged 47 commits intomainNBChub/bgcflow:mainfrom dev-0.6.0NBChub/bgcflow:dev-0.6.0Copy head branch name to clipboardJan 30, 2023

+15,307-53

Commits

Commits on Dec 16, 2022

• fix: rollback bigslice to v1.1.1

  matinnuhamunada

  committed
  f661583

• chore: bump to v0.5.2

  matinnuhamunada

  committed
  a5e0c5f

Commits on Dec 21, 2022

• feat: BiG-SCAPE update to 1.1.5 using MIBIG 3.1

  matinnuhamunada

  committed
  32c9a7b

• chore: correct logging

  matinnuhamunada

  committed
  a33c07d

• notebooks: add arts, cblaster, checkm, roary, and eggnog report template

  matinnuhamunada

  committed
  0216adf

Commits on Jan 8, 2023

• fix: correct bgc_ids from ARTS2 table

  matinnuhamunada

  committed
  88ca2f5

Commits on Jan 15, 2023

• feat: extract bgc table from antismash

  matinnuhamunada

  committed
  2dee08d

Commits on Jan 23, 2023

• notebook: update checkm figure with MIMAG classification

  matinnuhamunada

  committed
  0f2c62f

Commits on Jan 24, 2023

• feat: give better flexibility to choose project types

  matinnuhamunada

  committed
  389c8b5

Commits on Jan 26, 2023

• feat: introduce a bgc project type

  matinnuhamunada

  committed
  4d68caf

• feat: add interproscan and clinker

  matinnuhamunada

  committed
  34f88bc

• fix: correct genome_id naming

  matinnuhamunada

  committed
  81d3fcb

• chore: tidy logging info for gtdbtk and antismash install

  matinnuhamunada

  committed
  ed5a8da

• feat: add experimental Dockerfile

  matinnuhamunada

  committed
  5a35456

• fix: add working Dockerfile and Dockerhub link

  matinnuhamunada

  committed
  4879e9d

Commits on Jan 27, 2023

• fix: enable multiple bgc_id from the same genome_id

  matinnuhamunada

  committed
  0ecd126

• chore: use input path for variable changelog

  matinnuhamunada

  committed
  56370f1

• feat: add parameter max cluster size for roary

  matinnuhamunada

  committed
  8330ae5

Commits on Jan 28, 2023

• test: rename to tests to accomodate unit tests

  matinnuhamunada

  committed
  527a330

• test: add arts_extract unit test

  matinnuhamunada

  committed
  f77e3b5

• test: add fix_gtdb_taxonomy test

  matinnuhamunada

  committed
  066674a

• test: add gtdb_prep test

  matinnuhamunada

  committed
  0b09fc1

• fix: add missing config files for tests

  matinnuhamunada

  committed
  6363392

• test: add mash_convert test

  matinnuhamunada

  committed
  e3262fa

• test: add fastani_convert test

  matinnuhamunada

  committed
  2f4dea4

• test: add deeptfactor_to_json test

  matinnuhamunada

  committed
  3f70103

• test: add extract_ncbi_information test

  matinnuhamunada

  committed
  bbd8d68

• test: add antismash_overview_gather test

  matinnuhamunada

  committed
  d6e7f10

• test: remove on-success and try out pytest action

  matinnuhamunada

  committed
  584f772

• test: add coverage report

  matinnuhamunada

  committed
  1d2bc3a

• test: fix coverage report commentator

  matinnuhamunada

  committed
  1ad4d54

• feat: add Snakefile to run Metabase

  matinnuhamunada

  committed
  a3126c1

• fix: stop showing roary plot

  matinnuhamunada

  committed
  68d686b

• notebook: update eggnog reports

  matinnuhamunada

  committed
  9f2de0a

Commits on Jan 29, 2023

• test: add lactobacillus minimal example

  matinnuhamunada

  committed
  346d0b7

• fix: correct java and perl requirement for interproscan

  matinnuhamunada

  committed
  a41a0ca

• fix: don't include mibig in bigscape for BGCs

  matinnuhamunada

  committed
  beb4dbc

• chore: use conda with JDK for metabase

  matinnuhamunada

  committed
  c1299a4

• fix: pin gsl to 2.6 for mash

  matinnuhamunada

  committed
  a23398f

Commits on Jan 30, 2023

• chore: correct logging

  matinnuhamunada

  committed
  014a38f

• fix: correct zip location for BGC schema

  matinnuhamunada

  committed
  49ab2e6

• notebook: update np.matrix to np.asarray and fix eggnog

  matinnuhamunada

  committed
  519e1aa

• fix: rollback duckdb to version 38

  matinnuhamunada

  committed
  f04e8ff

• temporary_fix: use experimental dbt branch

  matinnuhamunada

  committed
  f207901

• fix: make sure parquet is flat to process in duckdb

  matinnuhamunada

  committed
  454325e

• chore: pin dbt repo to v0.1.0 release

  matinnuhamunada

  committed
  2d256f8

• Merge branch 'main' into dev-0.6.0

  matinnuhamunada

  authored
  285dfa3