Reorganize docs on running the pipeline. (#610)

* Reorganize docs on running the pipeline.

* Update page descriptions.

* Revert all cost-related updates

* Fix quick start link.

* Reorganize & improve run/overview & fix broken links.

* Add a note on supporting GCP only.

website/docs/execmodes/_category_.json → website/docs/advanced/development/_category_.json

@@ -1,6 +1,6 @@
 {
-  "label": "Execution modes",
-  "position": 3,
+  "label": "Development",
+  "position": 6,
   "link": {
     "type": "generated-index"
   }

website/docs/advanced/development/cromwell.md

@@ -0,0 +1,43 @@
+---
+title: Cromwell
+description: Running GATK-SV on Cromwell
+sidebar_position: 0
+---
+
+# Cromwell
+
+[Cromwell](https://github.com/broadinstitute/cromwell) is a workflow management system
+that takes a workflow (e.g., a workflow written in [Workflow Description Language (WDL)](https://openwdl.org)), 
+its dependencies and input data, and runs it on a given platform 
+(e.g., [GCP](https://cromwell.readthedocs.io/en/stable/backends/Google/)). 
+In order to run a workflow on Cromwell, you need a running instance of 
+Cromwell that is available in two forms: [Server and stand-alone mode](https://cromwell.readthedocs.io/en/stable/Modes/).
+
+In general, you may use a managed Cromwell server maintained by your 
+institute or host a self-managed server, or run Cromwell as a standalone Java application.
+The former is ideal for large scale execution in a managed environment, 
+and the latter is useful for small scale and isolated WDL development.
+
+:::info
+Due to its dependency on cloud-hosted resources and large-scale execution needs,
+we currently do not support running the entire GATK-SV pipeline using 
+Cromwell as a [stand-alone Java application](https://cromwell.readthedocs.io/en/stable/Modes/#run).
+
+Additionally, we currently only support running the pipeline on 
+Google Cloud Platform (GCP).
+:::
+
+# Cromwell Server
+
+There are two option to communicate with a running Cromwell server: 
+[REST API](https://cromwell.readthedocs.io/en/stable/tutorials/ServerMode/), and
+[Cromshell](https://github.com/broadinstitute/cromshell) which is a command line tool
+to interface with a Cromwell server. We recommend using Cromshell due to its simplicity 
+of use. This documentation is explained using Cromshell, but the same steps can be 
+taken using the REST API.
+
+- **Setup Cromwell**: You may follow [this](https://cromwell.readthedocs.io/en/stable/Modes/) documentation
+  on setting up a Cromwell server.
+
+- **Setup Cromshell**: You may follow [this](https://github.com/broadinstitute/cromshell) documentation
+  on installing and configuring Cromshell to communicate with the Cromwell server. 

website/docs/gs/docker.md

@@ -1,7 +1,7 @@
 ---
 title: Docker Images
 description: GATK-SV Docker Images
-sidebar_position: 3
+sidebar_position: 4
 slug: ./dockers
 ---
 

website/docs/gs/input_files.md

@@ -1,7 +1,7 @@
 ---
 title: Input Data
 description: Supported input and reference data.
-sidebar_position: 3
+sidebar_position: 5
 slug: ./inputs
 ---
 

website/docs/gs/overview.md

@@ -11,4 +11,4 @@ on Illumina short-read whole-genome sequencing (WGS) data.
 The pipeline genotypes structural variations using Docker-based tools, modularized in 
 different components, and orchestrated using Cromwell.
 
-The pipeline runs in two modes: [Cohort](/docs/execmodes/cohort) and [single-sample](/docs/execmodes/singlesample). 
+Please refer to the documentation on [this page](/docs/run/overview) for running the pipeline.  

website/docs/gs/runtime_env.md

@@ -49,38 +49,3 @@ and share code on forked repositories. Here are a some considerations:
   Local backends may not have the resources to execute all of the workflows. 
   Workflows that use fewer resources or that are less parallelized may be more successful. 
   For instance, some users have been able to run [GatherSampleEvidence](#gather-sample-evidence) on a SLURM cluster.
-
-# Cromwell
-
-[Cromwell](https://github.com/broadinstitute/cromwell) is a workflow management system
-that takes a workflow (e.g., a workflow written in [Workflow Description Language (WDL)](https://openwdl.org)), 
-its dependencies and input data, and runs it on a given platform 
-(e.g., [GCP](https://cromwell.readthedocs.io/en/stable/backends/Google/)). 
-In order to run a workflow on Cromwell, you need a running instance of 
-Cromwell that is available in two forms: [Server and stand-alone mode](https://cromwell.readthedocs.io/en/stable/Modes/).
-
-In general, you may use a managed Cromwell server maintained by your 
-institute or host a self-managed server, or run Cromwell as a standalone Java application.
-The former is ideal for large scale execution in a managed environment, 
-and the latter is useful for small scale and isolated WDL development.
-
-:::info
-Due to its dependency on cloud-hosted resources and large-scale execution needs,
-we currently do not support running the entire GATK-SV pipeline using 
-Cromwell as a [stand-alone Java application](https://cromwell.readthedocs.io/en/stable/Modes/#run) 
-:::
-
-# Cromwell Server
-
-There are two option to communicate with a running Cromwell server: 
-[REST API](https://cromwell.readthedocs.io/en/stable/tutorials/ServerMode/), and
-[Cromshell](https://github.com/broadinstitute/cromshell) which is a command line tool
-to interface with a Cromwell server. We recommend using Cromshell due to its simplicity 
-of use. This documentation is explained using Cromshell, but the same steps can be 
-taken using the REST API.
-
-- **Setup Cromwell**: You may follow [this](https://cromwell.readthedocs.io/en/stable/Modes/) documentation
-  on setting up a Cromwell server.
-
-- **Setup Cromshell**: You may follow [this](https://github.com/broadinstitute/cromshell) documentation
-  on installing and configuring Cromshell to communicate with the Cromwell server. 

website/docs/modules/evidence_qc.md

@@ -11,7 +11,7 @@ The results from this module can be used for QC and batching.
 For large cohorts, this workflow can be run on arbitrary cohort 
 partitions of up to about 500 samples. Afterwards, we recommend 
 using the results to divide samples into smaller batches (~100-500 samples) 
-with ~1:1 male:female ratio. Refer to the [Batching](/docs/run/batching) section 
+with ~1:1 male:female ratio. Refer to the [Batching](/docs/run/joint#batching) section 
 for further guidance on creating batches.
 
 We also recommend using sex assignments generated from the ploidy 

website/docs/run/batching.md → website/docs/run/joint.md

@@ -1,9 +1,16 @@
 ---
-title: Batching
-description: Batching
-slug: batching
+title: Joint-calling
+description: Run the pipeline on a cohort
+sidebar_position: 4
+slug: joint
 ---
 
+:::info
+This documentation page is incomplete, and we are actively working on improving it with comprehensive information.
+:::
+
+## Batching
+
 For larger cohorts, samples should be split up into batches of about 100-500 
 samples with similar characteristics. We recommend batching based on overall 
 coverage and dosage score (WGD), which can be generated in [EvidenceQC](/docs/modules/eqc). 

website/docs/run/overview.md

@@ -0,0 +1,48 @@
+---
+title: Overview
+description: Overview
+sidebar_position: 1
+slug: overview
+---
+
+There are two factors to consider when deciding how to run GATK-SV. 
+
+
+1. **Variant calling modes: single-sample and cohort-based calling.**
+  GATK-SV offers two distinct pipeline configurations for detecting 
+  structural variations (SVs), each tailored for different research needs:
+
+    - **Single-sample analysis:** 
+      This configuration is ideal for examining SVs in individual samples, 
+      focusing exclusively on data from that single sample. Running this mode is less complex, 
+      involving just one workflow per sample.
+
+    - **Joint calling:** 
+      This configuration is designed for more extensive studies, such as those 
+      involving population genetics or disease association studies. 
+      It analyzes SVs across a cohort by collectively assessing data from all samples. 
+      However, this comes with increased complexity compared to the single-sample mode, 
+      requiring the execution of multiple workflows and involves data preparation steps 
+      (e.g., batching files from the cohort).
+
+
+2. **Which platform you would like to use for running GATK-SV?** 
+   You may run GATK-SV on the following platforms. 
+
+   - [Terra.bio](https://terra.bio): A user-friendly cloud-native platform for scalable data analysis. 
+     The primary focus of this documentation is on supporting the execution of GATK-SV within the Terra platform.
+
+   - [Cromwell](https://github.com/broadinstitute/cromwell): 
+     You may run GATK-SV on a self-hosted and managed cromwell instance, which is ideal for 
+     power-users and developers. We provide guidelines for this option in the 
+     [_advanced guides_](/docs/advanced/development/cromwell) section.
+
+
+Your decision regarding the execution modes and platform should be guided by 
+the objectives of your study, the size of your cohort, data access needs, 
+and the trade-off between a straightforward interface (Terra) 
+and more detailed customization options (self-managed Cromwell server). 
+Please refer to the following documentation on running GATK-SV within the Terra platform.
+
+- [Single-sample on Terra](single.md);
+- [Joint calling on Terra](joint.md).

website/docs/run/single.md

@@ -0,0 +1,14 @@
+---
+title: Single-sample
+description: Run the pipeline on a single sample
+sidebar_position: 3
+slug: single
+---
+
+:::info
+This documentation page is incomplete, and we are actively working on improving it with comprehensive information.
+:::
+
+We have developed a 
+  [Terra workspace](https://app.terra.bio/#workspaces/help-gatk/GATK-Structural-Variants-Single-Sample)
+for running GATK-SV on a single sample, which contains the related documentation.

website/src/pages/index.js

@@ -17,7 +17,7 @@ function HomepageHeader() {
         <div className={styles.buttons}>
           <Link
             className="button button--secondary button--lg"
-            to="/docs/intro">
+            to="/docs/gs/qs">
             Quick Start
           </Link>
         </div>