Outdated PBTA Histologies v20 : Run molecular subtyping

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Run molecular subtyping for v20 release

What was your approach?

• rerun to get up-to-date collapse files that are not pushed to git ../analyses/collapse-rnaseq/run-collapse-rnaseq.sh
• rerun all sutyping https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/c66d5c56b32c190ae6f8f5873773f54f60a17bc9/scripts/run-for-subtyping.sh#L36-L69

What GitHub issue does your pull request address?

1048

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

Which areas should receive a particularly close look?

• Most unexpected changes are from CNV alteration updates ( probably direct results of manta filtering update #1116) additional input/verification might be needed since it affects subtypes

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)?

tables

What is your summary of the results?

• 7316-2686 is added to EWS sutyping https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1032
• Fusion_counts and Fusion_evidence was added to HGG sutypes output from #1094
• lgat and hgat metadata results file are changed because of we removed the extra columns previous_cancer_predispositions previous_parent_aliquot_id #1079

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.

[jharenza]

these issues are now being addressed in #1127