v12 ATRT subtyping (11/N)

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR reruns ATRT subtyping. This module is solely based on methylation.

What was your approach?

Minor code changes to format the ATRT subtypes and pull the new methylation column names.
Major code changes to reformat output to one specimen per line.

What GitHub issue does your pull request address?

v12 subtyping and d3b-center/ticket-tracker-OPC#505

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

Which areas should receive a particularly close look?

Updated code

Is there anything that you want to discuss further?

No

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

Yes

Results

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

Results table:
N tumors subtyped:

# A tibble: 4 x 2
  molecular_subtype          n
  <chr>                  <int>
1 ATRT, MYC                 20
2 ATRT, SHH                 22
3 ATRT, To be classified    57
4 ATRT, TYR                 11

What is your summary of the results?

This module is solely based on methylation.

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.

[sangeetashukla]

The logic is sound, the results are justified. Approving.

[atlas4213]

The code logic looks good to me and the module ran correctly