feat: cohort building release 1

[mkirk111]

Addition of cohort feature page for PeCan
Cleanup of a few items no longer applicable.

[stjudecloud-cloudy]

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[Copilot]

🟡 Changes recommended

Several documentation issues, including contradictory usage guidance and missing front matter, remain unresolved.

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Pull request overview

Adds PeCan cohort-building documentation, expands data-facet and PIE guides, and updates release notes and related guidance.

Changes:

• Added cohort-building, data-facet, and PIE documentation.
• Updated FAQs, terminology, sample counts, and navigation metadata.
• Removed obsolete platform guidance and updated release notes.

File summaries

File	Reviewed change
content/4.pecan/6.release-notes/1.index.md	Added cohort release notes; list formatting needs correction.
content/4.pecan/6.release-notes/_dir.yml	Updated release notes navigation.
content/4.pecan/5.pecan-pie/2.faq.md	Added PIE FAQ; file-size and compression guidance is contradictory.
content/4.pecan/5.pecan-pie/1.what-is-pie.md	Added PIE guide; contains malformed table tags and minor typos.
content/4.pecan/5.pecan-pie/_dir.yml	Updated PIE navigation.
content/4.pecan/3.data-facets/5.use-cases.md	Updated facet use-case terminology.
content/4.pecan/3.data-facets/4.histology.md	Added histology documentation; figure numbering needs correction.
content/4.pecan/3.data-facets/3.expression.md	Added expression documentation.
content/4.pecan/3.data-facets/2.mutational-signatures.md	Added mutational-signature documentation; corrected FIFO wording and typo needed.
content/4.pecan/3.data-facets/1.variants.md	Added variants documentation; contains spelling and acronym corrections.
content/4.pecan/3.data-facets/_dir.yml	Updated data-facet navigation.
content/4.pecan/2.cohort-building/1.cohort-building.md	Added cohort guide; front matter, link syntax, and punctuation require correction.
content/4.pecan/2.cohort-building/_dir.yml	Added cohort navigation title.
content/4.pecan/1.overview/4.faq.md	Updated cohort FAQ.
content/4.pecan/1.overview/2.methods-and-data.md	Updated sample-count information.
content/4.pecan/1.overview/1.getting-started.md	Updated navigation terminology; facet-list punctuation needs correction.
content/3.genomics-platform/1.getting-started/1.overview.md	Removed obsolete Slack guidance.
content/1.overview/4.faq.md	Updated citation guidance.

Review details

Suppressed comments (3)

content/4.pecan/2.cohort-building/1.cohort-building.md:1

• This page is the only PeCan content page without front matter (title/navigation metadata). As a result, it will not have the metadata used by the documentation navigation/search (the sibling facet pages all declare it), so the new Cohort Building page may be omitted or displayed without a title. Add front matter before the heading.

# Cohort Building

content/4.pecan/2.cohort-building/1.cohort-building.md:8

• The link destination starts with a space (]( https://...)), so the Markdown link is not reliably parsed as a valid URL and may render as plain text or an invalid href. Remove the whitespace after (.

If you don't have a St. Jude Cloud account, you can find the account creation steps in our documentation. [Creating a St. Jude Cloud Account]( https://docs.stjude.cloud/genomics-platform/getting-started/accounts-and-billing#creating-a-st-jude-cloud-account)

content/4.pecan/6.release-notes/1.index.md:22

• These feature entries use Unicode bullets and o markers rather than Markdown list syntax, so they render as ordinary paragraph text instead of the intended nested list. Use -/indented - list markers here so the release notes retain their structure.

• Files reviewed: 9/25 changed files
• Comments generated: 2
• Review effort level: Lite

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