Update jhu_ntap (Hirbe) datataset

[anngvu]

Issue to track updating hirbe dataset previous submitted (#1). (Note: the curators assigned the directory name nst_nfosi_ntap, this dataset is referenced as jhu because that is easier for us to remember.)

Changelog / Notes

(most recent changes on top)

• Revise dataset to remove samples below, update case list again
• Create first pass staging dataset, send out case list to confirm -- should remove JH-2-084 and JH-2-106
• (Clinical data) Use most updated clinical data: syn53354432 Replace with even more up-to-date Biobank-batch1234-NF1status-Stavriani-10272023.xlsx - syn53646453
• (RNA-seq gene expression) Add counts from https://www.synapse.org/#!Synapse:syn53141534.1/datasets/
• (MAF) Use updated MAFs from https://www.synapse.org/#!Synapse:syn51907770

Checklist

• Format and replace with files noted in changelog
• Regenerate case list
  GCL=path/to/directory/with/script python2 $GCL/generate_case_lists.py -c $GCL/case_list_conf.txt -d case_lists -s . -i nst_nfosi_ntap -o
• Validate with suitable version of images
  docker run --rm -v $(pwd):/datahub cbioportal/cbioportal:4.1.13 validateStudies.py -d /datahub -l nst_nfosi_ntap -u http://cbioportal.org -html /datahub/nst_nfosi_ntap/html_report
• Get approval
• Create mirror issue in cBioPortal/datahub (cBioPortal requirement): Update current study nst_nfosi_ntap with new samples, data cBioPortal/datahub#2034
• Make PR that passes checks: Update nfosi jhu dataset cBioPortal/datahub#2035

[anngvu]

@jaybee84 Closing this, we can start watching the PR cBioPortal#2035.

[jaybee84]

Just want to mention that this refers to the JHU Biobank dataset which is from Christine Pratilas's Lab in Hopkins. They collaborated with Dr. Angela Hirbe for data generation. So maybe calling it Pratilas dataset (instead of Hirbe dataset) would reduce confusion going forward.