From 2ce5889e1fe9d9647b32399d336cc90b3a9bb3f6 Mon Sep 17 00:00:00 2001
From: rxu17 <26471741+rxu17@users.noreply.github.com>
Date: Wed, 8 Jan 2025 11:53:32 -0800
Subject: [PATCH] Add to param docstrings (#165)

* add to param docstrings

* add missing true
---
 nextflow_schema.json      | 4 ++--
 scripts/uploads/README.md | 8 ++++++++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index e1f694a..f2679ba 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -37,7 +37,7 @@
                 },
                 "production": {
                     "type": "boolean",
-                    "description": "Whether to run in production mode or not. Production mode means uploading to Synapse.",
+                    "description": "Uploads to production project or not (staging project).",
                     "default": false,
                     "enum": [
                         true,
@@ -57,7 +57,7 @@
                 },
                 "use_grs": {
                     "type": "boolean",
-                    "description": "Whether to use grs as primary mapping (dd as secondary) or not (using dd only). ",
+                    "description": "Whether to use grs as primary mapping (dd as secondary) or not (using dd only).",
                     "default": false,
                     "enum": [
                         true,
diff --git a/scripts/uploads/README.md b/scripts/uploads/README.md
index 95e480c..5546e3f 100644
--- a/scripts/uploads/README.md
+++ b/scripts/uploads/README.md
@@ -93,6 +93,9 @@ Options:
 
         --production
                 Whether to run in production mode or not (staging mode).
+
+        --use_grs
+                Whether to use grs as primary mapping (dd as secondary) or not (using dd only).
 ```
 
 Example run (staging run):
@@ -105,6 +108,11 @@ Example run (production run):
 Rscript merge_and_uncode_rca_uploads.R -c NSCLC -u -a $SYNAPSE_AUTH_TOKEN --production
 ```
 
+Example run (production run) using grs:
+```
+Rscript merge_and_uncode_rca_uploads.R -c NSCLC -u -a $SYNAPSE_AUTH_TOKEN --production --use_grs true
+```
+
 ## Usage: remove patient IDs from a REDCap formatted file
 
 To display the command line interface: