🔨 Missed updates improvements

Many updates to reflect changes in file locations, file inputs, and old and new studies:

• Updated README with latest info
• Updated config styles of older studies
• Removed deprecated configs
• Updated data processing and and pbta_all to handle DGD inputs
• Updated pipeline script to run data collations steps in parallel
• Removed deprecated fusion script
• Updated convert sv to handle current DGD format
• Updated pipeline script to handle new DGD formats
• Updated download script to handle multiple aws keys and also be able to pull from sbg at the same time

What's Changed

• Feature/mb missed updates improvements by @migbro in #33

Full Changelog: v0.6.0...v0.7.0

v0.6.0 SV Format Updates

• Added openpbta processing scripts (might have been from @sakshamphul )
• Updated configs with new SV format
• Added new refs to config
• Added new refs
• Mild improvements to cnv scripts
• Updated sv script to handle openX input
• Added new sv script to wrapper pipeline
• Updated Bo's perl script to handle new input reference
• Added functionality to download script

What's Changed

• 🛠 update sv format by @migbro in #32

Full Changelog: v0.5.1...v0.6.0

🐛 Fixed extra blank column output

In the faster and more efficient cpp plugin for z score, there was an output bug in which an extra blank column was added. This fixes that.

What's Changed

• fix the cpp bug by @sakshamphul in #31

Full Changelog: v0.5.0...v0.5.1

✨ v0.5.0 New studies and tool

• Added open_chordoma study and config
• Updated configs
• Improved download script with better error handling
• Made SV output script for fusions production-ready

What's Changed

• 🛠 add open chordoma, upgrade sv by @migbro in #30

Full Changelog: v0.4.0...v0.5.0

🛠 Ref updates, tool updates, new study configs

Made a few upgrades and improvements:

• Added new refs to reflect annotation upgrades
• Added config files for Chrodoma study updates
• Updated download script to also download from cavatica instead of s3 bucket

What's Changed

• 🛠 Ref updates, tool updates, new study configs by @migbro in #29

Full Changelog: v0.3.1...v0.4.0

🔧 Minor bug fix

• Fixed openpbta config file
• Added script to convert openX manifest to data_clinical files

What's Changed

• Add meninigioma study config file to the ETL by @sakshamphul in #24
• Add Utility scripts from openpbta study run by @sakshamphul in #26
• Zscore by @sakshamphul in #25
• Add an argument to let user decide the computation method: C++/R by @sakshamphul in #27
• 🔧 fixed pbta config by @migbro in #28

New Contributors

• @sakshamphul made their first contribution in #24

Full Changelog: v0.3.0...v0.3.1

Study ETL Updates

Study ETL Updates

• OpenPedCan
  • Added blacklist option for histology-to-clinical datasheets script
  • Added option to set minimum samples needed to create a cohort/histology-specific case list
  • Updated documentation to better reflect what was done
• OpenPBTA
  • Removed reliance on parent_aliquot_id ID filed to name samples as the column no longer exists in histology file
• pbta_all
  • Dropped DGD due to QC issues

New Study addition

Added pbta_all_treatment

• Same as pbta_all except has treatment-related entries in config
• Still beta, so only to be loaded into QA

What's Changed

• Feature/open pedcan v11 by @migbro in #22
• Feaure/mb add timeline by @migbro in #23

Full Changelog: v0.2.3...v0.3.0

New Configs + bug fix

• Fixed tumor type conversion for OpenPedCan project
• Added studies aml_sd_z6mwd3h0_2018 and os_sd_zxjffmef_2015)

New Study + Config

New AML study added plus enhancements to the config file for upstream capabilities.

New beta release

Added a config file for the oligo study load

What's Changed

• 🎉 added oligo study config by @migbro in #13

Full Changelog: v0.2...v0.2.1