feat: updated mdx learn links (#3328)

docs/events/bioconductor-popup-workshops-20210426.mdx

@@ -21,7 +21,7 @@ The main goal is to engage and enable the use of AnVIL / Terra by R users. All s
 
 ## Tutorials and Videos
 
-For a tutorial based on the workshop with an accompanying tutorial see [Using R / Bioconductor in AnVIL](/learn/data-analysts/using-r-bioconductor-in-anvil).
+For a tutorial based on the workshop with an accompanying tutorial see [Using R / Bioconductor in AnVIL](/learn/interactive-analysis/using-r-bioconductor-in-anvil).
 
 ## To Register
 

docs/events/bioconductor-popup-workshops-20210503.mdx

@@ -21,7 +21,7 @@ The main goal is to engage and enable the use of AnVIL / Terra by R users. All s
 
 ## Tutorials and Videos
 
-For a tutorial based on the workshop with an accompanying tutorial see [The R / Bioconductor AnVIL Package for Easy Access to Buckets, Data, and Workflows, and Fast Package Installation](/learn/data-analysts/the-r-bioconductor-anvil-package).
+For a tutorial based on the workshop with an accompanying tutorial see [The R / Bioconductor AnVIL Package for Easy Access to Buckets, Data, and Workflows, and Fast Package Installation](/learn/interactive-analysis/the-r-bioconductor-anvil-package).
 
 ## To Register
 

docs/events/bioconductor-popup-workshops-20210510.mdx

@@ -21,7 +21,7 @@ The main goal is to engage and enable the use of AnVIL / Terra by R users. All s
 
 ## Tutorials and Videos
 
-For a tutorial based on the workshop with an accompanying tutorial see [Running a Workflow: Bulk RNASeq Differential Expression from FASTQ Files to Top Table](/learn/data-analysts/running-a-workflow).
+For a tutorial based on the workshop with an accompanying tutorial see [Running a Workflow: Bulk RNASeq Differential Expression from FASTQ Files to Top Table](/learn/interactive-analysis/running-a-workflow).
 
 ## To Register
 

docs/events/bioconductor-popup-workshops-20210517.mdx

@@ -21,7 +21,7 @@ The main goal is to engage and enable the use of AnVIL / Terra by R users. All s
 
 ## Tutorials and Videos
 
-For a tutorial based on the workshop with an accompanying tutorial see [Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in R / Bioconductor](/learn/data-analysts/single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-r-bioconductor).
+For a tutorial based on the workshop with an accompanying tutorial see [Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in R / Bioconductor](/learn/interactive-analysis/single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-r-bioconductor).
 
 ## To Register
 

docs/events/bioconductor-popup-workshops-20210524.mdx

@@ -21,7 +21,7 @@ The main goal is to engage and enable the use of AnVIL / Terra by R users. All s
 
 ## Tutorials and Videos
 
-For a tutorial based on the workshop with an accompanying tutorial see [Using AnVIL for teaching R / Bioconductor](/learn/data-analysts/using-anvil-for-teaching-r-bioconductor).
+For a tutorial based on the workshop with an accompanying tutorial see [Using AnVIL for teaching R / Bioconductor](/learn/interactive-analysis/using-anvil-for-teaching-r-bioconductor).
 
 ## To Register
 

docs/events/bioconductor-popup-workshops-20210531.mdx

@@ -21,7 +21,7 @@ The main goal is to engage and enable the use of AnVIL / Terra by R users. All s
 
 ## Tutorials and Videos
 
-For a tutorial based on the workshop with an accompanying tutorial see [Reproducible research with AnVILPublish](/learn/data-analysts/reproducible-research-with-anvilpublish).
+For a tutorial based on the workshop with an accompanying tutorial see [Reproducible research with AnVILPublish](/learn/interactive-analysis/reproducible-research-with-anvilpublish).
 
 ## To Register
 

docs/faq/data-submission.mdx

@@ -18,9 +18,9 @@ AnVIL aims to host a variety of datasets useful to the genomics community. Submi
 ## Who pays for storage costs in AnVIL?
 
 AnVIL will cover storage costs of data from NHGRI funded studies that has been or will be released publicly to the research community (including those registered in dbGaP or DUOS and released through controlled access). Otherwise, storage costs are incurred by the billing account associated with the workspace.
-For more on understanding and controlling cloud costs in AnVIL, see [Understanding Cloud Costs](/learn/introduction/understanding-cloud-costs).
+For more on understanding and controlling cloud costs in AnVIL, see [Understanding Cloud Costs](/learn/cloud-costs/understanding-cloud-costs).
 
-For more on preparing a budget justification for cloud costs in AnVIL, see [Budget Templates](/learn/investigators/budget-templates).
+For more on preparing a budget justification for cloud costs in AnVIL, see [Budget Templates](/learn/cloud-costs/budget-templates).
 
 ## Does NHGRI plan to move data from dbGaP to AnVIL?
 

docs/learn/cloud-costs/budget-templates.mdx

@@ -17,7 +17,7 @@ Google Cloud Platform charges fees for:
 1. **Computing** - Compute costs are driven by CPU and memory usage. See [Standard Machine Types](https://cloud.google.com/compute/all-pricing#n1_standard_machine_types) for more information and current pricing.
 
 <Alert icon={false} severity="info">
-    For more information and a broader overview of cloud costs, see [Understanding Cloud Costs](/learn/introduction/understanding-cloud-costs).
+    For more information and a broader overview of cloud costs, see [Understanding Cloud Costs](/learn/cloud-costs/understanding-cloud-costs).
 </Alert>
 
 ## Estimating your Cloud Costs

docs/learn/getting-started/creating-a-google-cloud-billing-account.mdx

@@ -24,7 +24,7 @@ Google Cloud Billing Accounts allow you to configure payment and track spending
 
 Before setting up your Google Cloud Billing Account:
 
-1. Decide what email address to use. The email you choose must be associated with a Google ID (see [Obtaining a Google ID](/learn/account-setup/obtaining-a-google-id)) and must be the email you will use to log in to Terra.
+1. Decide what email address to use. The email you choose must be associated with a Google ID (see [Obtaining a Google ID](/learn/getting-started/obtaining-a-google-id)) and must be the email you will use to log in to Terra.
 1. Decide what payment method (credit card, debit card, PayPal, or bank account) you will use.
 1. Determine if you will set up as an individual or business. If you are setting up an account for a company, organization, lab, or institution, select "Business." If you are setting up as yourself, choose "Individual."
 

docs/learn/getting-started/creating-a-terra-account.mdx

@@ -6,7 +6,7 @@ description: ""
 title: "Creating a Terra Account"
 ---
 
-To register for a Terra account, you will need a Gmail account or another email account (an institutional email, for example) associated with a Google identity for SSO. See [Obtaining a Google Id](/learn/account-setup/obtaining-a-google-id) for instructions on creating a Google ID.
+To register for a Terra account, you will need a Gmail account or another email account (an institutional email, for example) associated with a Google identity for SSO. See [Obtaining a Google Id](/learn/getting-started/obtaining-a-google-id) for instructions on creating a Google ID.
 
 See [Set up a Terra account](https://support.terra.bio/hc/en-us/articles/360028235911-How-to-register-for-a-Terra-account) for instructions on setting up your Terra account.
 

docs/learn/getting-started/setting-up-lab-accounts.mdx

@@ -35,8 +35,8 @@ Knowledge of these concepts and how they interrelate will help you implement the
 Critical concepts for review are:
 
 1. **Terra Workspaces and Permissions** - For an overview of Terra workspaces, workspace permissions, and general billing information, see [ Getting Started with AnVIL](/learn).
-1. **Cloud Cost Basics** - For an overview of cloud costs, see [Understanding Cloud Costs](/learn/introduction/understanding-cloud-costs).
-1. **Billing Concepts** - For an overview of Google Cloud Platform and Terra billing concepts, see [Overview of Billing Concepts](/learn/billing-setup/billing-concepts).
+1. **Cloud Cost Basics** - For an overview of cloud costs, see [Understanding Cloud Costs](/learn/cloud-costs/understanding-cloud-costs).
+1. **Billing Concepts** - For an overview of Google Cloud Platform and Terra billing concepts, see [Overview of Billing Concepts](/learn/getting-started/billing-concepts).
 
 ## Lab Setup Design
 
@@ -135,13 +135,13 @@ Once lab members have a Google ID, they can use that email address to create a T
 
 To create a Terra account:
 
-1. Follow the instructions provided in the [Account Setup Guide](/learn/account-setup/overview-of-account-setup).
+1. Follow the instructions provided in the [Account Setup Guide](/learn/getting-started/overview-of-account-setup).
 
 ### 3 - Create Your Lab’s Google Billing Accounts
 
 <Alert severity="warning">
   If this is your first Google Billing Account, see [Creating a Google Billing
-  Account](/learn/billing-setup/creating-a-google-cloud-billing-account) for a
+  Account](/learn/getting-started/creating-a-google-cloud-billing-account) for a
   walk-through of the first-time flow. Use the instructions below to add
   additional accounts.
 </Alert>

docs/learn/interactive-analysis/getting-started-with-bioconductor.mdx

@@ -54,13 +54,13 @@ The [AnVIL package](https://bioconductor.org/packages/AnVIL) R / Bioconductor pa
 
 The following Terra / AnVIL R / Bioconductor Popup Workshops were held in 2021 from April to June.
 
-- Week 1: [Using R / Bioconductor in AnVIL](/learn/data-analysts/using-r-bioconductor-in-anvil) with Martin Morgan
-- Week 2: [The R / Bioconductor AnVIL Package](/learn/data-analysts/the-r-bioconductor-anvil-package) with Martin Morgan and Nitesh Turaga
-- Week 3: [Running a Workflow](/learn/data-analysts/running-a-workflow) with Martin Morgan and Kayla Interdonato
-- Week 4: [Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in R / Bioconductor](/learn/data-analysts/single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-r-bioconductor) with Vince Carey
-- Week 5: [Using AnVIL for Teaching R](/learn/data-analysts/using-anvil-for-teaching-r-bioconductor) with Levi Waldron
-- Week 6: [Reproducible Research with AnVILPublish](/learn/data-analysts/reproducible-research-with-anvilpublish) with Martin Morgan
-- Week 7: [Participant Stories](/learn/data-analysts/participant-stories)
+- Week 1: [Using R / Bioconductor in AnVIL](/learn/interactive-analysis/using-r-bioconductor-in-anvil) with Martin Morgan
+- Week 2: [The R / Bioconductor AnVIL Package](/learn/interactive-analysis/the-r-bioconductor-anvil-package) with Martin Morgan and Nitesh Turaga
+- Week 3: [Running a Workflow](/learn/interactive-analysis/running-a-workflow) with Martin Morgan and Kayla Interdonato
+- Week 4: [Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in R / Bioconductor](/learn/interactive-analysis/single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-r-bioconductor) with Vince Carey
+- Week 5: [Using AnVIL for Teaching R](/learn/interactive-analysis/using-anvil-for-teaching-r-bioconductor) with Levi Waldron
+- Week 6: [Reproducible Research with AnVILPublish](/learn/interactive-analysis/reproducible-research-with-anvilpublish) with Martin Morgan
+- Week 7: [Participant Stories](/learn/interactive-analysis/participant-stories)
 
 [Introduction to the Terra AnVIL Cloud-based Genomics Platform](https://youtu.be/N83iDYE2yQM) by Sehyun Oh and Levi Waldron at Bioc2021
 

docs/learn/interactive-analysis/reproducible-research-with-anvilpublish.mdx

@@ -14,7 +14,7 @@ An exploration of elements of reproducible research with the AnVILPublish packag
   <AlertTitle>Notes</AlertTitle>
 
   1. Visit the [course schedule](/events/bioconductor-popup-workshops-20210531#other-sessions) for links to the recorded session, and to other workshops in the series.
-  1. The material below requires a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Next Steps](/learn/data-analysts/reproducible-research-with-anvilpublish#next-steps)' for how to create a billing account.
+  1. The material below requires a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Next Steps](/learn/interactive-analysis/reproducible-research-with-anvilpublish#next-steps)' for how to create a billing account.
   1. Access to the workspaces we use may require registration; please [sign up](https://forms.gle/HCY2DM2QsuxAwdhv6) with your AnVIL email address.
 
 </Alert>

docs/learn/interactive-analysis/running-a-workflow.mdx

@@ -16,7 +16,7 @@ How to configure and run a workflow, based on the Bioconductor-Workflow-DESeq2 w
   <AlertTitle>Notes</AlertTitle>
 
   1. Visit the [course schedule](/events/bioconductor-popup-workshops-20210510#other-sessions) for links to the recorded session, and to other workshops in the series.
-  1. The material below requires a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Next Steps](/learn/data-analysts/running-a-workflow#next-steps)' for how to create a billing account.
+  1. The material below requires a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Next Steps](/learn/interactive-analysis/running-a-workflow#next-steps)' for how to create a billing account.
   1. Access to the workspaces we use may require registration; please [sign up](https://forms.gle/HCY2DM2QsuxAwdhv6) with your AnVIL email address.
 
 </Alert>

docs/learn/interactive-analysis/single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-r-bioconductor.mdx

@@ -212,7 +212,7 @@ Notice the colData entry label.ont. We can use this mapping of cell types to the
 
 ![Mapping Cell Types to Cell Ontology](/consortia/learn/data-analysts/analysis-mapping-cell-types.png)
 
-This just shows the positions in a portion of the Cell Ontology, of the first 20 cell types. See [Appendix 1](/learn/data-analysts/single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-r-bioconductor#appendix-1-sketching-ontological-relationships) for details on how this is done.
+This just shows the positions in a portion of the Cell Ontology, of the first 20 cell types. See [Appendix 1](/learn/interactive-analysis/single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-r-bioconductor#appendix-1-sketching-ontological-relationships) for details on how this is done.
 
 To conclude the exploration, answer the following questions:
 

docs/learn/interactive-analysis/the-r-bioconductor-anvil-package.mdx

@@ -16,7 +16,7 @@ An exploration of how workspaces provide a framework for managing data and large
   <AlertTitle>Notes</AlertTitle>
 
   1. Visit the [course schedule](/events/bioconductor-popup-workshops-20210503#other-sessions) for links to the recorded session, and to other workshops in the series.
-  1. The material below requires a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Next Steps](/learn/data-analysts/the-r-bioconductor-anvil-package#next-steps)' for how to create a billing account.
+  1. The material below requires a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Next Steps](/learn/interactive-analysis/the-r-bioconductor-anvil-package#next-steps)' for how to create a billing account.
   1. Access to the workspaces we use may require registration; please [sign up](https://forms.gle/HCY2DM2QsuxAwdhv6) with your AnVIL email address.
 
 </Alert>
@@ -36,7 +36,7 @@ This week we'll explore how workspaces provide a framework for managing data and
 
 ### Previously...
 
-- Notes and recorded session: [Using R / Bioconductor in AnVIL](/learn/data-analysts/using-r-bioconductor-in-anvil)
+- Notes and recorded session: [Using R / Bioconductor in AnVIL](/learn/interactive-analysis/using-r-bioconductor-in-anvil)
 
 ### Essential Steps
 

docs/learn/interactive-analysis/using-anvil-for-teaching-r-bioconductor.mdx

@@ -15,7 +15,7 @@ A case study of using AnVIL to teach R for a Biostatistics course and provides e
 <Alert icon={false} severity="info">
   <AlertTitle>Notes</AlertTitle>
 
-  1. Doing this on your own will require a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Set up Billing](/learn/data-analysts/using-anvil-for-teaching-r-bioconductor#set-up-billing)' for options to create a billing account.
+  1. Doing this on your own will require a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Set up Billing](/learn/interactive-analysis/using-anvil-for-teaching-r-bioconductor#set-up-billing)' for options to create a billing account.
   1. Access to the workspace we use requires registration; please [sign up](https://forms.gle/HCY2DM2QsuxAwdhv6) with your AnVIL email address.
 
 </Alert>
@@ -114,7 +114,7 @@ Steps:
 
 This course setup is GitHub-centric and uses AnVIL/Terra only as an end-user computing environment. It pulls data from GitHub or other online resources and does not use the AnVIL/Terra workspace for anything other than providing compute.
 
-This setup is more complicated than you probably need: for most instructors, a single course GitHub repo would probably suffice, and you probably don’t need a course Docker image. In the simplest possible setup, create a single (private or public) course repo, and skip down to the section "[Post AnVIL/Terra instructions to students](/learn/data-analysts/using-anvil-for-teaching-r-bioconductor#post-anvilterra-instructions-to-students)."
+This setup is more complicated than you probably need: for most instructors, a single course GitHub repo would probably suffice, and you probably don’t need a course Docker image. In the simplest possible setup, create a single (private or public) course repo, and skip down to the section "[Post AnVIL/Terra instructions to students](/learn/interactive-analysis/using-anvil-for-teaching-r-bioconductor#post-anvilterra-instructions-to-students)."
 
 ![GitHub Actions](/consortia/learn/data-analysts/using-anvil-github-actions.png)
 

docs/learn/interactive-analysis/using-r-bioconductor-in-anvil.mdx

@@ -15,7 +15,7 @@ An introduction to the AnVIL cloud computing environment. We learn how to create
 <Alert icon={false} severity="info">
   <AlertTitle>Notes</AlertTitle>
 
-  1. The material below requires a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Next Steps](/learn/data-analysts/using-r-bioconductor-in-anvil#next-steps)' for how to create a billing account.
+  1. The material below requires a billing account. We provide a billing account during the workshop, but if you're following along on your own see '[Next Steps](/learn/interactive-analysis/using-r-bioconductor-in-anvil#next-steps)' for how to create a billing account.
   1. Access to the workspace we use requires registration; please [sign up](https://forms.gle/HCY2DM2QsuxAwdhv6) with your AnVIL email address.
 
 </Alert>

docs/learn/introduction/guides-and-tutorials.mdx

@@ -13,8 +13,8 @@ Key guides and tutorials grouped by user persona are listed below. For a general
 
 ### Investigators
 
-- [Setting Up Lab Accounts](/learn/investigators/setting-up-lab-accounts) - Follow these instructions to get your accounts, set up billing, and set up your team members to do research with AnVIL.
-- [Creating Cloud Cost Budget Justifications](/learn/investigators/budget-templates) - Templates for calculating a cloud cost budget and writing a budget justification for using AnVIL in your grant applications.
+- [Setting Up Lab Accounts](/learn/getting-started/setting-up-lab-accounts) - Follow these instructions to get your accounts, set up billing, and set up your team members to do research with AnVIL.
+- [Creating Cloud Cost Budget Justifications](/learn/cloud-costs/budget-templates) - Templates for calculating a cloud cost budget and writing a budget justification for using AnVIL in your grant applications.
 
 ### Data Analysts
 

docs/news/2021/03/10/announcing-seqr-in-anvil.mdx

@@ -21,7 +21,7 @@ With the onset of key NHGRI datasets being ingested to AnVIL such as Center for
 ## Using Seqr in AnVIL
 
 Researchers will need to bring their joint call files to the AnVIL to make use of Seqr.
-If a joint call file is needed, researchers can use [GATK tooling](/learn/anvil-mooc/use-case-gatk), also available within AnVIL.
+If a joint call file is needed, researchers can use [GATK tooling](/learn/analysis-workflows/use-case-gatk), also available within AnVIL.
 
 To launch Seqr on a Terra workspace, navigate to the workspaces' "Data" tab, select the "Files" subtab, and select "Analyze in Seqr" in the top right of the page.
 

docs/news/2024/04/15/comparing-the-nhgri-anvil-platform.mdx

@@ -116,7 +116,7 @@ that AnVIL’s Azure users are accountable for cloud infrastructure expenses.
 
 A number of resources are available to users to help understand potential costs for working on the cloud.
 
-- [Preparing a Cloud Cost Budget Justification](/learn/investigators/budget-templates)
+- [Preparing a Cloud Cost Budget Justification](/learn/cloud-costs/budget-templates)
 
 For more information on costs and billing on GCP, read more here: