Code

Merge Bakta refactor into Dev#102

Code

Closed

kyleoconnell wants to merge 76 commits intomasterCDCgov/tostadas:masterfrom devCDCgov/tostadas:devCopy head branch name to clipboard

+54,956-356

Commits

Commits on Aug 10, 2023

• parameter for running the bakta annotation and the docker file for this

  ankushkgupta2

  committed
  69d7bdd

  Copy full SHA for 69d7bdd

• entrypoint for running bakta annotation added

  ankushkgupta2

  committed
  3455f49

  Copy full SHA for 3455f49

• checks for the bakta annotation parameter, docker parameter for this annotation, and the output directory are being checked now within general checks

  ankushkgupta2

  committed
  52174fa

  Copy full SHA for 52174fa

• same parameters within test_parameters set added with default params

  ankushkgupta2

  committed
  92604ea

  Copy full SHA for 92604ea

• module/process for calling BAKTA annotation directly created

  ankushkgupta2

  committed
  52519cd

  Copy full SHA for 52519cd

• module/process for calling BAKTA annotation directly created

  ankushkgupta2

  committed
  39df7db

  Copy full SHA for 39df7db

• entrypoint subworkflow for BAKTA created

  ankushkgupta2

  committed
  cdec147

  Copy full SHA for cdec147

Commits on Aug 25, 2023

• latest changes to gitignore and some changes for wget/yum aka downloading mambaforge packaged based on system

  ankushkgupta2

  committed
  2be515c

  Copy full SHA for 2be515c

• new diphtheria data to test with BAKTA

  ankushkgupta2

  committed
  e227920

  Copy full SHA for e227920

Commits on Sep 7, 2023

• relevant variola files - references fasta/gff + sequence fasta file

  

  Gupta

  committed
  d43af05

  Copy full SHA for d43af05

Commits on Sep 18, 2023

• bakta integration

  

  EC2 Default User

  committed
  1e8e307

  Copy full SHA for 1e8e307

Commits on Sep 19, 2023

• Merge branch '48-internal-bakta' into master

  Swarnali3

  authored
  2a79916

  Copy full SHA for 2a79916

• Merge pull request #74 from Swarnali3/master

  Show description for 8e8c63a
  Swarnali3

  authored
  8e8c63a

  Copy full SHA for 8e8c63a

• test:changes to bakta modules

  

  EC2 Default User

  committed
  9768d5e

  Copy full SHA for 9768d5e

Commits on Sep 20, 2023

• changes for metadata validation

  

  EC2 Default User

  committed
  de7c2f3

  Copy full SHA for de7c2f3

Commits on Sep 21, 2023

• test_params.config modified

  

  EC2 Default User

  committed
  e41e61b

  Copy full SHA for e41e61b

Commits on Oct 3, 2023

• splitting multi-fasta file upstream bakta

  

  EC2 Default User

  committed
  af40a25

  Copy full SHA for af40a25

Commits on Oct 11, 2023

• splitting test config file into test_virus_params and test_bacteria_params files

  

  EC2 Default User

  committed
  ee7afdb

  Copy full SHA for ee7afdb

Commits on Oct 16, 2023

• bakta re-programmed to run with single fasta file

  

  EC2 Default User

  committed
  39cab38

  Copy full SHA for 39cab38

Commits on Oct 17, 2023

• changes made to module validate params to run bakta using bacterial test config file

  

  EC2 Default User

  committed
  cd1e756

  Copy full SHA for cd1e756

Commits on Oct 30, 2023

• gff post-transformation and integration in script

  

  EC2 Default User

  committed
  2e6f55e

  Copy full SHA for 2e6f55e

Commits on Nov 2, 2023

• change output gff3 file to gff file

  

  EC2 Default User

  committed
  ab7a80d

  Copy full SHA for ab7a80d

Commits on Nov 6, 2023

• changed the name of the workflow to main.nf vs mpxv.nf before and made the change within main.nf

  ankushkgupta2

  committed
  a414969

  Copy full SHA for a414969

Commits on Nov 10, 2023

• adding comments to python script for bakta

  

  EC2 Default User

  committed
  24b70f7

  Copy full SHA for 24b70f7

Commits on Nov 14, 2023

• adding module for repeatmasker and connecting to module for liftoff

  

  EC2 Default User

  committed
  7deea8e

  Copy full SHA for 7deea8e

Commits on Nov 17, 2023

• condition for variola or mpox specific repeat library added

  

  EC2 Default User

  committed
  8cba15f

  Copy full SHA for 8cba15f

• added liftoff cli and concat modules; implemented new python script to concat and correctly format liftoff and repeatmasker gff; added entry subworkflow for the repeatmasker_liftoff strategy and mo…

  Show description for 1780996
  

  zyosufzai

  committed
  1780996

  Copy full SHA for 1780996

• added more instructions to config files

  

  zyosufzai

  committed
  8391e97

  Copy full SHA for 8391e97

Commits on Dec 6, 2023

• changed the name of the file from mpxv.nf to main.nf + moved out the params log information to a separate module + this module is being called within the main workflow

  ankushkgupta2

  committed
  a834240

  Copy full SHA for a834240

• separate module for params help print out under general utility directory

  ankushkgupta2

  committed
  a1f4357

  Copy full SHA for a1f4357

• manually adding bc scicomp wont push

  kyleoconnell

  authored
  c116867

  Copy full SHA for c116867

• Add files via upload

  kyleoconnell

  authored
  a3e6034

  Copy full SHA for a3e6034

• Add files via upload

  kyleoconnell

  authored
  8076972

  Copy full SHA for 8076972

• updated docker container for pandas on concat_gff

  

  kyleaoconnell22

  committed
  7d3a9b1

  Copy full SHA for 7d3a9b1

• Merge pull request #91 from CDCgov/65-external-feature-running-variola-sequences-through-the-pipeline

  Show description for cbd3314
  kyleoconnell

  authored
  cbd3314

  Copy full SHA for cbd3314

• updated repeatmasker

  

  kyleaoconnell22

  committed
  15bbff8

  Copy full SHA for 15bbff8

• Merge pull request #84 from CDCgov/65-external-feature-running-variola-sequences-through-the-pipeline

  Show description for 74b25e9
  kyleoconnell

  authored
  74b25e9

  Copy full SHA for 74b25e9

• removed .ipynb checkpoints

  

  kyleaoconnell22

  committed
  de4405c

  Copy full SHA for de4405c

• removed ipynb checkpoints;

  

  kyleaoconnell22

  committed
  48e30b0

  Copy full SHA for 48e30b0

Commits on Dec 8, 2023

• updated bakta download module

  

  kyleaoconnell22

  committed
  b683160

  Copy full SHA for b683160

• updated bakta workflow

  

  kyleaoconnell22

  committed
  312df46

  Copy full SHA for 312df46

• added new bakta functionality

  

  kyleaoconnell22

  committed
  cbbbb09

  Copy full SHA for cbbbb09

Commits on Dec 10, 2023

• added two new parameters within metadata validation python script: custom_field_values and custom_field_types (both are list types)

  ankushkgupta2

  committed
  6318a46

  Copy full SHA for 6318a46

• added new parameter: samples_to_apply_custom, which is a list type and contains sample names to apply custom field checks to

  ankushkgupta2

  committed
  81b8f45

  Copy full SHA for 81b8f45

• latest code for metadata validation dynamic fields + new / modified input files for testing custom fields

  ankushkgupta2

  committed
  3a7132e

  Copy full SHA for 3a7132e

• changes to the sample metadata sheet continaing the custom fields, for testing purposes

  ankushkgupta2

  committed
  6b7f937

  Copy full SHA for 6b7f937

• refined / refactored some of the code + fixed issues with passing certain configurations within the custom fields yaml/json

  ankushkgupta2

  committed
  9b03e87

  Copy full SHA for 9b03e87

• placed validation_outputs directory output within the base dir, aka /validation_outputs/, just to mitigate for testing reasons... need to eventually clean up this .gitignore file to be much cleaner…

  Show description for 9b0eb34
  ankushkgupta2

  committed
  9b0eb34

  Copy full SHA for 9b0eb34

Commits on Dec 11, 2023

• created a separate directory for custom meta fields related files, inclues the modified metadata sample sheet with custom fields and an example .json file

  ankushkgupta2

  committed
  bd93790

  Copy full SHA for bd93790

• general refactoring + based on tests, made changes to handle if a column is being renamed multiple times

  ankushkgupta2

  committed
  47b6ded

  Copy full SHA for 47b6ded

• moved files to separate directory

  ankushkgupta2

  committed
  3eb3484

  Copy full SHA for 3eb3484

• updated the parameter sets for standard and test to include validate_custom_fields and custom_fields_file for the dynamic metadata fields

  ankushkgupta2

  committed
  bf3b322

  Copy full SHA for bf3b322

• added a default path for the custom fields file

  ankushkgupta2

  committed
  0ccc472

  Copy full SHA for 0ccc472

• added new nextflow params for dynamic metadata fields to remaining parameter sets

  ankushkgupta2

  committed
  5731ab0

  Copy full SHA for 5731ab0

• merged latest variola/repeat masker updates that were pushed into dev

  ankushkgupta2

  committed
  676dd41

  Copy full SHA for 676dd41

• old information / commits added back to file

  ankushkgupta2

  committed
  35f24a6

  Copy full SHA for 35f24a6

• Merge pull request #88 from CDCgov/77-internal-move-help-message

  Show description for d774c84
  ankushkgupta2

  authored
  d774c84

  Copy full SHA for d774c84

• Merge remote-tracking branch 'origin/dev' into 58-internal-dynamic-metadata

  ankushkgupta2

  committed
  2d15096

  Copy full SHA for 2d15096

• removed lingering piece of code for checking outputs

  ankushkgupta2

  committed
  3eca13b

  Copy full SHA for 3eca13b

• had the wrong file name for the default path value for the custom_fields_file

  ankushkgupta2

  committed
  33e1dec

  Copy full SHA for 33e1dec

• removed uncessary explicit listing of .nextflow.log files and just used a *

  ankushkgupta2

  committed
  231a2e5

  Copy full SHA for 231a2e5

• under some comments, put some encoding information, might potentially use in the future

  ankushkgupta2

  committed
  f52f276

  Copy full SHA for f52f276

• changed the default path for custom_fields_file to the correct one, was pointing to the metadata file before

  ankushkgupta2

  committed
  7970afd

  Copy full SHA for 7970afd

• added parameters for custom fields

  ankushkgupta2

  committed
  895acba

  Copy full SHA for 895acba

• latest changes

  ankushkgupta2

  committed
  f7db7d1

  Copy full SHA for f7db7d1

• refactoring bakta

  

  kyleaoconnell22

  committed
  867bd62

  Copy full SHA for 867bd62

• Merge pull request #92 from CDCgov/58-internal-dynamic-metadata

  Show description for e2204a7
  kyleoconnell

  authored
  e2204a7

  Copy full SHA for e2204a7

• added samplesheet

  

  kyleaoconnell22

  committed
  ae9b4ff

  Copy full SHA for ae9b4ff

• added input channel for bakta db

  

  kyleaoconnell22

  committed
  aac7eb1

  Copy full SHA for aac7eb1

• Merge branch 'dev' of github.com:CDCgov/tostadas into 48-internal-bakta

  kyleoconnell

  committed
  760154f

  Copy full SHA for 760154f

• Merge pull request #93 from CDCgov/48-internal-bakta

  Show description for 28f6916
  kyleoconnell

  authored
  28f6916

  Copy full SHA for 28f6916

• patched bakta entrypoint

  kyleoconnell

  committed
  4a4603e

  Copy full SHA for 4a4603e

Commits on Dec 12, 2023

• Merge branch 'dev' into bakta_refactor_kao

  kyleoconnell

  authored
  f8d1162

  Copy full SHA for f8d1162

Commits on Dec 13, 2023

• Merge pull request #94 from CDCgov/bakta_refactor_kao

  Show description for e6e86e3
  ankushkgupta2

  authored
  e6e86e3

  Copy full SHA for e6e86e3

Commits on Dec 15, 2023

• fixed formatting error

  kyleoconnell

  committed
  de7ef72

  Copy full SHA for de7ef72

Commits on Jan 3, 2024

• syncing local changes

  kyleoconnell

  committed
  5b7d470

  Copy full SHA for 5b7d470