add molecular subtype to wgs-only samples

komalsrathi commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

WGS only samples are missing medulloblastoma molecular subtype info. They need to be annotated as "To be Classified"

What was your approach?

Added a separate script to append wgs-only samples to the output tsv files

What GitHub issue does your pull request address?

https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1183

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

Which areas should receive a particularly close look?

04-no-RNA-samples.R and output tsv files

Is there anything that you want to discuss further?

N/A

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)?

tsv files

What is your summary of the results?

N/A

Reproducibility Checklist

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

Documentation Checklist

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

jaclyn-taroni commented 2 years ago

Just to note, these changes won't take effect unless we cut another release, correct?

jharenza commented 2 years ago

Just to note, these changes won't take effect unless we cut another release, correct?

I wasn't thinking of another release, but just adding them to our histologies file in the supplement. Do you want us to rerun subtyping and do another release for that to happen?

jaclyn-taroni commented 2 years ago

I don't think we want to be in a situation where the release and the supplemental data are out of sync, but perhaps the new release can be the very last thing we do before we cut a release of the codebase.

jharenza commented 2 years ago

I don't think we want to be in a situation where the release and the supplemental data are out of sync, but perhaps the new release can be the very last thing we do before we cut a release of the codebase.

Ok, sounds good - put in #1207 for this

AlexsLemonade / OpenPBTA-analysis