Move documentation to website

wdl/GenotypeBatch.wdl

@@ -28,7 +28,7 @@ workflow GenotypeBatch {
     File? pesr_exclude_list  # Required unless skipping training
     File splitfile
     File? splitfile_index
-    String? reference_build  #hg19 or hg38, Required unless skipping training
+    String? reference_build  # Must be hg38, Required unless skipping training
     File bin_exclude
     File ref_dict
     # If all specified, training will be skipped (for single sample pipeline)

website/docs/acknowledgements.md

@@ -0,0 +1,18 @@
+---
+title: Acknowledgements
+description: Acknowledgements
+sidebar_position: 10
+---
+
+The following resources were produced using data from the [All of Us Research Program](https://allofus.nih.gov/) 
+and have been approved by the Program for public dissemination:
+
+* Genotype filtering model: "aou_recalibrate_gq_model_file" in "inputs/values/resources_hg38.json"
+
+The All of Us Research Program is supported by the National Institutes of Health, Office of the Director: Regional 
+Medical Centers: 1 OT2 OD026549; 1 OT2 OD026554; 1 OT2 OD026557; 1 OT2 OD026556; 1 OT2 OD026550; 1 OT2 OD 026552; 1 
+OT2 OD026553; 1 OT2 OD026548; 1 OT2 OD026551; 1 OT2 OD026555; IAA #: AOD 16037; Federally Qualified Health Centers: 
+HHSN 263201600085U; Data and Research Center: 5 U2C OD023196; Biobank: 1 U24 OD023121; The Participant Center: U24 
+OD023176; Participant Technology Systems Center: 1 U24 OD023163; Communications and Engagement: 3 OT2 OD023205; 3 OT2 
+OD023206; and Community Partners: 1 OT2 OD025277; 3 OT2 OD025315; 1 OT2 OD025337; 1 OT2 OD025276. In addition, the All 
+of Us Research Program would not be possible without the partnership of its participants.

website/docs/advanced/_category_.json

@@ -1,6 +1,6 @@
 {
   "label": "Advanced Guides",
-  "position": 8,
+  "position": 9,
   "link": {
     "type": "generated-index"
   }

website/docs/advanced/build_inputs.md

@@ -1,7 +1,7 @@
 ---
 title: Building inputs
 description: Building work input json files
-sidebar_position: 1
+sidebar_position: 3
 slug: build_inputs
 ---
 
@@ -43,8 +43,6 @@ You may run the following commands to get these example inputs.
        └── test
    ```
 
-## Building inputs for specific use-cases (Advanced)
-
 ### Build for batched workflows
 
 ```shell
@@ -55,69 +53,3 @@ python scripts/inputs/build_inputs.py \
   -a '{ "test_batch" : "ref_panel_1kg" }'
 ```
 
-
-### Generating a reference panel
-
-This section only applies to the single-sample mode. 
-New reference panels can be generated from a single run of the 
-`GATKSVPipelineBatch` workflow. 
-If using a Cromwell server, we recommend copying the outputs to a 
-permanent location by adding the following option to the 
-[workflow configuration](https://cromwell.readthedocs.io/en/latest/wf_options/Overview/) 
-file:
-
-```json
-"final_workflow_outputs_dir" : "gs://my-outputs-bucket",
-"use_relative_output_paths": false,
-```
-
-Here is an example of how to generate workflow input jsons from `GATKSVPipelineBatch` workflow metadata:
-
-1. Get metadata from Cromwshell.
-
-   ```shell
-   cromshell -t60 metadata 38c65ca4-2a07-4805-86b6-214696075fef > metadata.json
-   ```
-
-2. Run the script. 
-
-   ```shell
-   python scripts/inputs/create_test_batch.py \
-      --execution-bucket gs://my-exec-bucket \
-      --final-workflow-outputs-dir gs://my-outputs-bucket \
-      metadata.json \
-      > inputs/values/my_ref_panel.json
-   ```
-
-3. Build test files for batched workflows (google cloud project id required).
-
-   ```shell
-   python scripts/inputs/build_inputs.py \
-      inputs/values \
-      inputs/templates/test \
-      inputs/build/my_ref_panel/test \
-      -a '{ "test_batch" : "ref_panel_1kg" }'
-   ```
-
-4. Build test files for the single-sample workflow
-
-   ```shell
-   python scripts/inputs/build_inputs.py \
-       inputs/values \
-       inputs/templates/test/GATKSVPipelineSingleSample \
-       inputs/build/NA19240/test_my_ref_panel \
-       -a '{ "single_sample" : "test_single_sample_NA19240", "ref_panel" : "my_ref_panel" }'
-   ```
-
-5. Build files for a Terra workspace.
-
-   ```shell 
-   python scripts/inputs/build_inputs.py \
-      inputs/values \
-      inputs/templates/terra_workspaces/single_sample \
-      inputs/build/NA12878/terra_my_ref_panel \
-      -a '{ "single_sample" : "test_single_sample_NA12878", "ref_panel" : "my_ref_panel" }'
-   ```
-
-Note that the inputs to `GATKSVPipelineBatch` may be used as resources 
-for the reference panel and therefore should also be in a permanent location.

website/docs/advanced/build_ref_panel.md

@@ -0,0 +1,73 @@
+---
+title: Building reference panels
+description: Building reference panels for the single-sample pipeline
+sidebar_position: 4
+slug: build_ref_panel
+---
+
+A custom reference panel for the [single-sample mode](/docs/gs/calling_modes#single-sample-mode) can be generated most easily using the
+[GATKSVPipelineBatch](https://github.com/broadinstitute/gatk-sv/blob/main/wdl/GATKSVPipelineBatch.wdl) workflow. 
+This must be run on a standalone Cromwell server, as the workflow is unstable on Terra. 
+
+:::note
+Reference panels can also be generated by running the pipeline through joint calling on Terra, but there is
+currently no solution for automatically updating inputs.
+:::
+
+We recommend copying the outputs from a Cromwell run to a permanent location by adding the following option to 
+the workflow configuration file:
+```
+  "final_workflow_outputs_dir" : "gs://my-outputs-bucket",
+  "use_relative_output_paths": false,
+```
+
+Here is an example of how to generate workflow input jsons from `GATKSVPipelineBatch` workflow metadata:
+
+1. Get metadata from Cromwshell.
+
+   ```shell
+   cromshell -t60 metadata 38c65ca4-2a07-4805-86b6-214696075fef > metadata.json
+   ```
+
+2. Run the script.
+
+   ```shell
+   python scripts/inputs/create_test_batch.py \
+      --execution-bucket gs://my-exec-bucket \
+      --final-workflow-outputs-dir gs://my-outputs-bucket \
+      metadata.json \
+      > inputs/values/my_ref_panel.json
+   ```
+
+3. Build test files for batched workflows (google cloud project id required).
+
+   ```shell
+   python scripts/inputs/build_inputs.py \
+      inputs/values \
+      inputs/templates/test \
+      inputs/build/my_ref_panel/test \
+      -a '{ "test_batch" : "ref_panel_1kg" }'
+   ```
+
+4. Build test files for the single-sample workflow
+
+   ```shell
+   python scripts/inputs/build_inputs.py \
+       inputs/values \
+       inputs/templates/test/GATKSVPipelineSingleSample \
+       inputs/build/NA19240/test_my_ref_panel \
+       -a '{ "single_sample" : "test_single_sample_NA19240", "ref_panel" : "my_ref_panel" }'
+   ```
+
+5. Build files for a Terra workspace.
+
+   ```shell 
+   python scripts/inputs/build_inputs.py \
+      inputs/values \
+      inputs/templates/terra_workspaces/single_sample \
+      inputs/build/NA12878/terra_my_ref_panel \
+      -a '{ "single_sample" : "test_single_sample_NA12878", "ref_panel" : "my_ref_panel" }'
+   ```
+
+Note that the inputs to `GATKSVPipelineBatch` may be used as resources
+for the reference panel and therefore should also be in a permanent location.

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

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

website/docs/advanced/development/cromwell.md → website/docs/advanced/cromwell/overview.md

@@ -1,6 +1,6 @@
 ---
-title: Cromwell
-description: Running GATK-SV on Cromwell
+title: Overview
+description: Introduction to Cromwell
 sidebar_position: 0
 ---
 

website/docs/gs/quick_start.md → website/docs/advanced/cromwell/quick_start.md

@@ -1,18 +1,16 @@
 ---
-title: Quick Start
-description: Run the pipeline on demo data.
+title: Run
+description: Running GATK-SV on Cromwell
 sidebar_position: 1
 slug: ./qs
 ---
 
-This page provides steps for running the pipeline using demo data.
-
 # Quick Start on Cromwell
 
 This section walks you through the steps of running pipeline using 
 demo data on a managed Cromwell server.
 
-### Setup Environment
+### Environment Setup
 
 - A running instance of a Cromwell server.
 

website/docs/advanced/docker/_category_.json

@@ -1,6 +1,6 @@
 {
-  "label": "Docker Images",
-  "position": 7,
+  "label": "Docker builds",
+  "position": 2,
   "link": {
     "type": "generated-index"
   }

website/docs/best_practices.md

@@ -0,0 +1,18 @@
+---
+title: Best Practices Guide
+description: Guide for using GATK-SV
+sidebar_position: 4
+---
+
+A comprehensive guide for the single-sample calling mode is available in [GATK Best Practices for Structural Variation 
+Discovery on Single Samples](https://gatk.broadinstitute.org/hc/en-us/articles/9022653744283-GATK-Best-Practices-for-Structural-Variation-Discovery-on-Single-Samples).
+This material covers basic concepts of structural variant calling, specifics of SV VCF formatting, and 
+advanced troubleshooting that also apply to the joint calling mode as well. This guide is intended to supplement 
+documentation found here.
+
+Users should also review the [Getting Started](/docs/gs/overview) section before attempting to perform SV calling.
+
+The following sections also contain recommendations pertaining to data and call set QC:
+
+- Preliminary sample QC in the [EvidenceQc module](/docs/modules/eqc#preliminary-sample-qc).
+- Assessment of completed call sets can be found on the [MainVcfQc module page](/docs/modules/mvqc).

website/docs/run/_category_.json → website/docs/execution/_category_.json

@@ -1,5 +1,5 @@
 {
-  "label": "Run",
+  "label": "Execution",
   "position": 4,
   "link": {
     "type": "generated-index"