v12 embryonal subtyping (7/N)

[ewafula]

Purpose/implementation Section

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR runs Embryonal subtyping for v12

What was your approach?

made the following changes:

• Updated script 01 to include high-confidence methylation embryonal subtypes from the histologies base file where subtypes are either NA or CNS Embryonal, NOS
• Checked to confirm that all gene symbols utilized within the module are up to date with Gencode v39

NEW	OLD
TTYH1   TTYH1
MN1     MN1
FOXR2   FOXR2
CIC     CIC
PATZ1   PATZ1
LIN28A  LIN28A
BCOR    BCOR
HGNET   HGNET

• README updated.

What GitHub issue does your pull request address?

Part of the v12 release

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

Which areas should receive a particularly close look?

Please review scripts 01 and 04 in detail to ensure the logic is correct.

Is there anything that you want to discuss further?

NA

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)?

embryonal subtyping table output.

What is your summary of the results?

• embryonal_tumor_molecular_subtypes.tsv

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.

[kelseykeith]

Since this review was an ASAP request, just want to comment with a quick update. Code runs reproducibly and error-free and for samples that were subtyped both in v11 and this v12 rerun, subtypes match. However, there's only 8 samples that overlap between v11 and v12 so I'm just running down the differences there and then I will either request changes or approve.

[kelseykeith]

Never mind about the 8 samples, I was comparing the wrong files. Everything looks good:

• code runs correctly
• includes the same samples as v11 plus additional samples
• correctly replaces 'CNS Embryonal, NOS' with the methylation molecular subtype if available

[rjcorb]

LGTM! everything runs fine and logic is correct.