Hgg subtype update: Adding tp53 status

[kgaonkar6]

⚠️ merge after #942 is in master

Purpose/implementation Section

What scientific question is your analysis addressing?

Adding TP53 status along with evidence columns(tp53_XYZ from classifier,SNV and CNV calls to HGG samples.

What was your approach?

I am using tp53_nf1_score/results/tp53_altered_status.tsv to add the tp53_altered status to the subtypes already annotated to the sample_id

What GitHub issue does your pull request address?

#807

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jharenza]

I think that we want to capture any TP53-altered samples in the subtyping, rather than just loss. For HGG_molecular_subtype.tsv, will you also add TP53 activated?

[kgaonkar6]

I think that we want to capture any TP53-altered samples in the subtyping, rather than just loss. For HGG_molecular_subtype.tsv, will you also add TP53 activated?
will do!

[jharenza]

looks great, thank you!