Pipeline QC comments

[ao508]

TODO

• update MAF output filename to data_mutations_extended.txt
• update MAF meta filename to meta_mutations_extended.txt
• clinical file meta data headers must start with #
• CNA header should have Hugo_Symbol (header shows GENE SYMBOL)
• CNA file for test study has duplicate headers. Headers for data types like CNA and expression should be treated as if they might have duplicate sample ids just in case. Only use the first sample id you come across if a duplicate is found.
• extra file found in output directory called expression_cna.txt - this should not exist

For documentation:

• add reference to cBioPortal file formats in README.md so that anyone using the pipeline can reference the cbio docs to understand the file formats generated by the GDC pipeline