v3.0.1

Changes:

• Update version number to egg4_config_v2.1.6.py
• Update version number to dias_TWE_config_GRCh37_v3.0.1.json
• Updated the README.md to reflect latest names/versions used in the config

For both egg4_config_v2.1.6.py and dias_TWE_config_GRCh37_v3.0.1.json:

• Vep config updated to v1.1.11

v3.0.0

• file is now a .json config (compatible with eggd_dias_batch v3.0.0), not a python script
• SNV variant workbooks are now frozen on column N

⚠️ Note the old .py script (version 2.1.5) is still in the repo, so that annotation source updates can carry on before eggd_dias_batch v3 goes live in Jan 2024

v2.1.5

Update VEP config to v1.1.10
Restore gnomADe_nhomalt & gnomADg_nhomalt in workbook

See https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3039887362/egg4+dias+TWE+config+v2.1.5

v2.1.4

• Updated to latest VEP config file v1.1.9 file-GZk4G404j4fppZV46p3F1X2v

See https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3018194945/egg4_dias_TWE_config+v2.1.4

v2.1.3

• Removes undesirable gnomad-related columns from workbooks stage

See https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3017474049/egg4_dias_TWE_config+v2.1.3

v2.1.2

Update assay version

Update VEP config to twe_vep_config_v1.1.8.json (230926 - VEP TWE Config file v1.1.8 )

Update README

See - https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3011870721/egg4_dias_TWE_config+v2.1.2

v2.1.1

Update to latest deployed VEP config file, v1.1.7 (file-GZ4bB504j4fkvQ4vqQyz1b29).

More info: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/2999255325/egg4+dias+TWE+config+v2.1.1

v2.1.0

egg4_config_v2.1.0.py

• Update reports workflow ID to v2.1.0
• Update assay version number for TWE from 2.0.4 > 2.1.0
• Rename stage IDs for dias_reports to match new stage IDs in the workflow. These stage IDs are more self-explanatory of what the stage does.
• Include inputs to apps that are no longer specified in the workflows in the config.

README.md

• New section detailing what the config includes
• New section detailing the versions of files and workflows in the config, including the file names and DNAnexus file IDs.

v2.0.3

egg4_config_v2.0.2.py → egg4_config_v2.0.3.py

Update to latest deployed VEP config file, v1.1.5 (file-GXvb2Y04j4fjv6vf5yGFpXFj).

More info: https://cuhbioinformatics.atlassian.net/wiki/spaces/RD/pages/2967830529/egg4+dias+TWE+config+v2.0.3

v2.0.2

Updated to latest VEP config file v1.1.4 file-GXJy7F04j4fV8gj37qYgfFfg

More info: https://cuhbioinformatics.atlassian.net/browse/NG-122
https://cuhbioinformatics.atlassian.net/wiki/spaces/RD/pages/2955968513/egg4+dias+TWE+config+v2.0.2