Add TARGET studies

[jamesqo]

What?

Adds the following TARGET studies from GDC:

• alal_target_gdc (TARGET-ALL-P3)
• aml_target_gdc (TARGET-AML)
• bll_target_gdc (TARGET-ALL-P2)
• nbl_target_gdc (TARGET-NBL)
• os_target_gdc (TARGET-OS)
• wt_target_gdc (TARGET-WT)

The following TARGET projects were excluded because they lack mutation data:

• TARGET-ALL-P1
• TARGET-CCSK
• TARGET-RT

Clinical mappings were provided by @sbabyanusha here: ISB-CGC Clinical Mappings

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 study meta data complete? e.g. pmid, group of PUBLIC
• 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 files
• MAF is based on hg19
• MAF with 2 isoforms: uniprot and mskcc
• CNA data with meta files
• CNA segment data with meta files
• Expression data including z-scores with meta files
• Case-lists for all profiles.
• Manual checking (Niki or JJ): Triage or private Portal link here