[NO MERGE] TCGA + CPTAC Release v2

[jamesqo]

What?

See here for a list of changes: https://github.com/cBioPortal/nci-crdc-pipeline/pull/215

checks

For all pull requests:

• Passes validation

For a new study (in addition to above):

• Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
• Is the study meta data complete? e.g. pmid, citation
• Were all samples profiled with WES/WGS? If not, is gene panel file curated?
• Are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
• Clinical sample and patient data with meta files.
• Mutations data with meta file.
• Is the study based on hg38? If so, is the reference_genome: hg38 option included in meta study.
• CNA data with meta files
• CNA segment data with meta files
• Expression data including z-scores with meta files
• Other genomic profiles with meta files
• Case-lists for all profiles.
• Perform sanity checks based on the items in the checklist
• Manual checking (Niki or JJ): Triage or private Portal link here