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Plan for v0.6.1#226

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matinnuhamunada merged 53 commits intomainNBChub/bgcflow:mainfrom dev-0.6.1NBChub/bgcflow:dev-0.6.1Copy head branch name to clipboardJun 9, 2023

+2,256-290

Commits

Commits on Jan 30, 2023

• chore: initial commit for v0.6.1

  matinnuhamunada

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  d30836d

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Commits on Feb 18, 2023

• fix: pin numpy for GTDBtk

  matinnuhamunada

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  50503d0

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Commits on Mar 4, 2023

• fix: correct BGC compare workflow

  matinnuhamunada

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  8e9d84e

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• chore: correct automlst DAG

  matinnuhamunada

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  e0ed910

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• chore: add library for relationship transfer to metabase

  matinnuhamunada

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  31bb9a5

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• add instruction to transfer relationship to metabase

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  df5f590

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• fix: add nbextensions

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  769455c

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• fix: change table name

  matinnuhamunada

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  56b7e6d

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• feat: export all csv to parquet as warehouse

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  47f01fa

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• feat: upgrade metabase and database related functions

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  e0a8ba4

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• test: fix test change and visibility

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  35233c0

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Commits on Mar 9, 2023

• fix: correct bgc_id for data warehouse

  matinnuhamunada

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  a28d3df

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• fix: add figure statistics to roary report

  matinnuhamunada

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  adede14

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Commits on Mar 12, 2023

• fix: handle unusual sequence sart location

  matinnuhamunada

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  a4c7756

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Commits on Mar 13, 2023

• feat: add multi-threading for autoMLST wrapper

  matinnuhamunada

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  d454447

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• chore: clean up obsolette rules

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  ff4f5a7

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• chore: clean up refseq masher

  matinnuhamunada

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  daa354b

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• feat: upgrade automlst patch 0.1.1

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  7954ab9

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Commits on Mar 16, 2023

• notebook: use plotly and pygraphviz for ARTS2 report

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  3fceee2

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Commits on Mar 19, 2023

• fix: handle unusual locus tag location with characters and joints

  matinnuhamunada

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  1d80370

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• fix: enforce correct strain id using input

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  929f469

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• notebook: use graphviz sfdp layout to process large network

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  5a1cc0b

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• fix: correct genome_id preference in bgc overview

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  a25988a

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Commits on Apr 17, 2023

• fix: correct gtdb mjson when metadata and gtdb release are missing

  matinnuhamunada

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  9b61703

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• feat: BGC comparison with mmseqs2 and minimap

  matinnuhamunada

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  4ce130e

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• fix: use mix parameter fr bigscape in BGC comparison

  matinnuhamunada

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  5141da5

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• fix: update deeptfactor dependencies

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  2375ddd

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Commits on Apr 18, 2023

• fix: correct ARTS parameter to search for DUF and known resistance models

  matinnuhamunada

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  3d412b2

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Commits on Apr 20, 2023

• fix: correct path typo in arts rules

  matinnuhamunada

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  89000bd

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Commits on Apr 22, 2023

• fix: correct outfile generation for arts report

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  f16294f

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Commits on Apr 24, 2023

• notebook: update arts, cblaster, gtdbtk, and prokka-gbk report

  matinnuhamunada

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  eed6aa1

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• feat: copy summary and cds tsvs

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  ed06fc2

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• feat: add README in the processed folders

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  6638aa4

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Commits on Apr 27, 2023

• fix: add log prokka log summary and cds table

  matinnuhamunada

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  894ef88

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Commits on May 1, 2023

• fix: handle empty result for best k cluster

  matinnuhamunada

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  2369041

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Commits on May 2, 2023

• test: update gtdb CARD metadata

  matinnuhamunada

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  adf9f46

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• fix: update pytorch dependencies for deepTF

  matinnuhamunada

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  4efa2f0

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Commits on May 3, 2023

• feat: addadd path to region.csv

  matinnuhamunada

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  c492d37

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• test: update region format table output

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  09caa3d

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Commits on May 9, 2023

• fix: enforce samples csv metadata as string

  matinnuhamunada

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  148c87a

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• fix: enforce samples csv metadata as string

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  13d5da5

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Commits on May 10, 2023

• fix: avoid mistakes in cds region matching across contigs

  matinnuhamunada

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  6424fe9

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Commits on May 11, 2023

• fix: handle overlapping cds among two or more regions

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  6ce8386

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Commits on May 15, 2023

• feat: update bgc subworkflow rules

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  0b3d2e5

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• fix: correct input preparation for bgc subworkflow

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  822c47a

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• feat: include antismash region genbank name change in result

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  0f8b4f8

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Commits on May 18, 2023

• fix: handle missing gtdb entry release

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  82e41fc

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• fix: add details in metadata for selecting genomes in gtdbtk run

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  465dcac

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• tests: update gtdb prep

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  e43bb6a

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• chore: correct steps

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  50f833c

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Commits on May 22, 2023

• fix: correct GTDB version naming

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  131f324

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Commits on May 24, 2023

• fix: handle missing strains column

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  0311f54

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Commits on May 25, 2023

• fix: undo make temp files for prokka

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