Update formatting.

broadinstitute · Jun 4, 2024 · 17bbeb9 · 17bbeb9
1 parent 2a100a0
commit 17bbeb9
Showing 1 changed file with 74 additions and 36 deletions.
diff --git a/website/docs/advanced/build_inputs.md b/website/docs/advanced/build_inputs.md
@@ -53,47 +53,85 @@ You may run the following commands to get these example inputs.
        └── test
    ```
 
+## Building inputs for specific use-cases (Advanced)
 
-### build for batched workflows
+### Build for batched workflows
 
 ```shell
-python scripts/inputs/build_inputs.py inputs/values inputs/templates/test/GATKSVPipelineSingleSample inputs/build/NA19240/test -a '{ "test_batch" : "ref_panel_1kg", "cloud_env": "google_cloud.my_project" }'
+python scripts/inputs/build_inputs.py \
+  inputs/values \
+  inputs/templates/test/GATKSVPipelineSingleSample \
+  inputs/build/NA19240/test \
+  -a '{ "test_batch" : "ref_panel_1kg", "cloud_env": "google_cloud.my_project" }'
 ```
 
 
-### Generating a reference panel (Advanced, single-sample mode only)
-New reference panels can be generated easily 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 file:
-```
-  "final_workflow_outputs_dir" : "gs://my-outputs-bucket",
-  "use_relative_output_paths": false,
+### 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 p
+ermanent location by adding the following option to the workflow configuration 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:
-```
-> cromshell -t60 metadata 38c65ca4-2a07-4805-86b6-214696075fef > metadata.json
-> 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
-> # Define your google project id (for Cromwell inputs) and Terra billing project (for workspace inputs)
-> echo '{ "google_project_id": "my-google-project-id", "terra_billing_project_id": "my-terra-billing-project" }' > inputs/values/google_cloud.my_project.json
-> # Build test files for batched workflows (google cloud project id required)
-> python scripts/inputs/build_inputs.py \
-    inputs/values \
-    inputs/templates/test \
-    inputs/build/my_ref_panel/test \
-    -a '{ "test_batch" : "ref_panel_1kg", "cloud_env": "google_cloud.my_project" }'
-> # Build test files for the single-sample workflow
-> 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" }'
-> # Build files for a Terra workspace
-> 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.
+
+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. Define your google project id (for Cromwell inputs) and Terra billing project (for workspace inputs).
+
+   ```shell
+   echo '{ "google_project_id": "my-google-project-id", "terra_billing_project_id": "my-terra-billing-project" }' > inputs/values/google_cloud.my_project.json
+   ```
+
+4. 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", "cloud_env": "google_cloud.my_project" }'
+   ```
+
+5. 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" }'
+   ```
+
+6. 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.