V12 ews (6/N)

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR runs V12 EWS.

What was your approach?

Rerun and updated code to include methylation results. Note: only for PBTA and DGD.

What GitHub issue does your pull request address?

v12 release

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

Which areas should receive a particularly close look?

Please double check logic.

Is there anything that you want to discuss further?

This module uses EWS diagnosis or EWSR1 canonical fusions to find EWS diagnoses. I also added methylation subtype of EWS to this.

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)?

Table of subtypes.

What is your summary of the results?

88 bs_ids subtyped as EWS
Two of these are not EWS diagnoses and need further review with pathology.

BS_ER9RMSVG - this sample has MB diagnosis. It was To be classified via MB subtyping.
BS_SRW0DH5G - this sample has Cranio diagnosis. It was To be classified via Cranio subtyping.
These may be mis-diagnoses. Will need to confirm with pathology.

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]

This script logic looks consistent, and I agree the two samples listed in the PR need further investigation.

[zzgeng]

The code works well and logic is sound.

[atlas4213]

The code looks good to me and I see all the correct info in the output file