v17-Release

[baileyckelly]

Purpose/implementation Section

v17-Release to update the pbta-histologies file
closes #732

1. updated files description
2. updated release notes
3. Updated download script to point to v16/v17

What scientific question is your analysis addressing?

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What was your approach?

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What GitHub issue does your pull request address?

#637 Updated Histologies File
#631 LGAT subtyping
#623 EWS subtyping
#742 consensus of two classifiers for medulloblastoma

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

compare v16 & v17 histologies file

Which areas should receive a particularly close look?

all values were pulled fresh from the source databases so should be reviewed for changes vs v16

Is there anything that you want to discuss further?

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

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Results

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

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What is your summary of the results?

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Reproducibility Checklist

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• 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

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• 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.

Data Release Checklist

• Is the table in doc/data-file-descriptions.md up to date?
• Is doc/data-format.md up to date?
• Is doc/release-notes.md up to date?
• Is download-data.sh up to date?

[baileyckelly]

Made suggested changes to
Uploaded new md5.txt, release-notes.md, and pbta-histologies.tsv to S3.

[jaclyn-taroni]

@baileyckelly Apologies, we forgot about the update to the PBTA TMB file (pbta-snv-consensus-mutation-tmb-coding.tsv) post bug fix, etc. (#727 and #728). @cansavvy posted the updated file here: #732 (comment). This came to my attention when I was working on #765.

[jharenza]

@baileyckelly Apologies, we forgot about the update to the PBTA TMB file (pbta-snv-consensus-mutation-tmb-coding.tsv) post bug fix, etc. (#727 and #728). @cansavvy posted the updated file here: #732 (comment). This came to my attention when I was working on #765.

I will take care of this now.

[jharenza]

@jaclyn-taroni the download works and this is now ready for review. I semi-reviewed, but was also helping @baileyckelly, did some QC on the file, so requesting re-review!

[jaclyn-taroni]

The HGG molecular subtyping step is broken due to a v17 change to the histologies file. I commented that out in 2335db8. I am hoping that by getting past that step we can find anything else we need to resolve, fix or track it, merge #765, and then we'll get this in!

[jashapiro]

Looks good to me!