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add v14 release docs #507

Merged
merged 14 commits into from
Feb 7, 2020
Merged

add v14 release docs #507

merged 14 commits into from
Feb 7, 2020

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jharenza
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@jharenza jharenza commented Feb 3, 2020

Purpose/implementation Section

What scientific question is your analysis addressing?

Update v14 release docs

  • update release-notes.md
  • update data-files-description.md
  • update data-formats.md

What GitHub issue does your pull request address?

#432

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

Which areas should receive a particularly close look?

Do the docs look sufficient/am I missing anything?

Is there anything that you want to discuss further?

I updated the links to the D3b workflow repo because we renamed it for consistency with other repos and to not mix other publication workflows with this one.

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

Yes for docs - want to get OK so we can add these to S3.
No for data download.

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? - yes, but folder does not yet exist

Jo Lynne Rokita added 2 commits February 3, 2020 15:28
-update `release-notes.md`
-update `data-files-description.md`
-update `data-formats.md`
add new folder for V14 to download scipt
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@jharenza I think you might as well fold in the changes/feedback from #456 here. data-formats.md does not get distributed so that won't hold anything up.

Jo Lynne Rokita added 3 commits February 4, 2020 11:47
and description from @cansavvy [comments](#507 (comment))
- add removal of polyA+stranded samples that were still in file in v13
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jharenza commented Feb 4, 2020

@jaclyn-taroni I will work on #456 tonight. The data is now on s3, and download confirmed to work. Implemented @cansavvy changes in the docs. Ready for review!

@jharenza jharenza added the ready for review Used to label pull requests that are ready for review label Feb 4, 2020
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cansavvy commented Feb 4, 2020

@jharenza See #512

add more information on gistic output files, to replace PR [#456](#456)
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jharenza commented Feb 5, 2020

@jaclyn-taroni I updated the data-formats.md file with more GISTIC output info - I decided to only include potential relevant files that may be used, rather than all, and add some brief descriptions. Let me know if you would like more detail.

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@jharenza - in c48f340, I added links to the HGG and non-MB, non-ATRT embryonal tumor subtyping analysis modules. Am I correct that these are the only molecular subgroup labels that were updated in this release?

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jharenza commented Feb 5, 2020

yes, correct!

readme update for upcoming lancet MAF per issue [here](#512)
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jharenza commented Feb 5, 2020

We are re-running Lancet for TCGA, per the comment here - will update here once completed and updated on S3.

doc/release-notes.md Outdated Show resolved Hide resolved
yup, nice catch

Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Jo Lynne Rokita and others added 2 commits February 5, 2020 20:21
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:shipit:

@jaclyn-taroni jaclyn-taroni merged commit b82435a into master Feb 7, 2020
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3 participants