Adding support for CGC w/ Automation

[jordan-rash]

CC: @adthrasher

[adthrasher]

We can remove the IBC files:
IBC_CCDI/TCGABRCA_log2fpkm.SIG.txt
IBC_CCDI/GEP.195.quantileNormalized.geneLevel_log2.eset
IBC_CCDI/TCGABRCA_log2fpkm.TF.txt

@adamdingliang - Someone from your team will need to draft a description for the tool in CGC. See this example: https://cgc.sbgenomics.com/public/apps#ZCHONG/novobreak-commit/novobreak-analysis/. It would also be best to have helpful documentation for each of the input to the script (expression set, transcription factor network, signaling network, and metadata file). This should include information about the file formats and how to generate them. Ideally, it would also link to examples.

[adamdingliang]

We can remove the IBC files:
IBC_CCDI/TCGABRCA_log2fpkm.SIG.txt
IBC_CCDI/GEP.195.quantileNormalized.geneLevel_log2.eset
IBC_CCDI/TCGABRCA_log2fpkm.TF.txt

@adamdingliang - Someone from your team will need to draft a description for the tool in CGC. See this example: https://cgc.sbgenomics.com/public/apps#ZCHONG/novobreak-commit/novobreak-analysis/. It would also be best to have helpful documentation for each of the input to the script (expression set, transcription factor network, signaling network, and metadata file). This should include information about the file formats and how to generate them. Ideally, it would also link to examples.

Hi @adthrasher , I will work on the description. Thanks.

[jordan-rash]

We can remove the IBC files:
IBC_CCDI/TCGABRCA_log2fpkm.SIG.txt
IBC_CCDI/GEP.195.quantileNormalized.geneLevel_log2.eset
IBC_CCDI/TCGABRCA_log2fpkm.TF.txt

Done

[jordan-rash]

@adthrasher I just rebased and squashed the commits while dropping the GH change.....I am reviewing now, but another set of eyes is helpful....when I use the "Commit Changes" button in the UI, the commit log is not helpful, so I might have missed a piece

[adthrasher]

Just the small change to the environment secrets, then it looks good.

[adamdingliang]

Completed sanity check