feat: create c. auris / fungi paper (#806)

[frano-m]

Closes #806.

This pull request introduces a new featured analysis to the documentation and improves the styling of inline code elements in the Docs content. The most significant changes are the addition of a new analysis entry and the enhancement of code block appearance for better readability.

Documentation update:

• Added a new featured analysis entry titled "Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI: A Candidozyma auris Case Study" to featured-analyses.mdx.

Styling improvements:

• Introduced a new code CSS block to style inline code elements with a background color, inherited font size, and padding in content.styles.ts.
• Applied the new code styling to the StyledSectionContent component to ensure consistent inline code formatting throughout Docs content.

[Copilot]

Pull request overview

This pull request adds a new featured analysis for Candidozyma auris RNA-seq standardization to the documentation and improves the styling of inline code elements throughout the Docs content.

• Added a new featured analysis entry with supporting images for a C. auris case study
• Enhanced inline code styling with background color and padding for better readability
• Included four new webp images for the analysis visualization

Reviewed changes

Copilot reviewed 3 out of 9 changed files in this pull request and generated no comments.

File	Description
app/docs/learn/featured-analyses.mdx	Added new featured analysis entry for C. auris RNA-seq standardization with metadata and image reference
app/components/Docs/components/Content/content.styles.ts	Introduced CSS styling for inline code elements with background color, inherited font size, and padding
public/learn/featured-analyses/standardizing-rnaseq-candidozyma-auris/*.webp	Added four new webp images for visualization (binary files)

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[frano-m]

Hi @nekrut I’ve been working on the next fungi white paper and started adding references manually. I copied the REFERENCES.md file into the References section of the main document here. I wasn’t sure whether citations like @Santana2023 should link to the References section or directly to external sources (e.g. PubMed). In a few cases there wasn’t a direct match between the @… citation and the References section, so I linked out using the URLs in references.bib. Also, is there an automated way to generate reference linking, similar to what we used for the first white paper on measles? (cc: @dannon , @scottcain, @d-callan)

[Copilot]

Pull request overview

Copilot reviewed 3 out of 9 changed files in this pull request and generated no new comments.

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[nekrut]

Hi @nekrut I’ve been working on the next fungi white paper and started adding references manually. I copied the REFERENCES.md file into the References section of the main document here. I wasn’t sure whether citations like @Santana2023 should link to the References section or directly to external sources (e.g. PubMed). In a few cases there wasn’t a direct match between the @… citation and the References section, so I linked out using the URLs in references.bib. Also, is there an automated way to generate reference linking, similar to what we used for the first white paper on measles? (cc: @dannon , @scottcain, @d-callan)

The refs are here -> https://github.com/nekrut/whitePaper2/blob/main/references.bib I can format that any way you need - just me know.

[dannon]

I sync'd the content with the updated manuscript like @nekrut mentioned and fixed a couple issues:

Synced changes from nekrut/whitePaper2 MANUSCRIPT.md:

• Add missing author Junhao Qiu to author list
• Update Agentic AI section: "resist automation" -> "require custom
  analyses", expand LLM paragraph with two issues (artifact tracking +
  lack of agent framework), clarify "agentic coding tools"
• Add Nextflow and Snakemake citations to Discussion section, use
  "code-first workflow systems" terminology consistently
• Add Bioblend citation to Methods section for API interaction
• Change "native tools" -> "structured tools" for Galaxy tools

Proofing fixes:

• Add missing articles in introduction ("the external ear canal of a
  Japanese hospital patient")
• Remove errant article ("such as SARS-CoV-2" not "such as a SARS-CoV-2")
• Fix typo "dateset" -> "dataset"
• Fix line break in middle of word "showed"
• Use backticks for genome assembly ID to fix markdown rendering

(I should follow up and make sure those proofreading fixes make it back to the original manuscript, if they are there..)

[NoopDog]

Excellent, Thx!