From e500fe6a64bc8cdfb8d45bafd6687c69f31e851c Mon Sep 17 00:00:00 2001
From: rxu17 <26471741+rxu17@users.noreply.github.com>
Date: Tue, 29 Oct 2024 02:08:45 -0700
Subject: [PATCH] change comment shorthand

---
 modules/merge_and_uncode_rca_uploads.nf        | 4 ++--
 scripts/uploads/merge_and_uncode_rca_uploads.R | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/merge_and_uncode_rca_uploads.nf b/modules/merge_and_uncode_rca_uploads.nf
index 6507da93..9ce69550 100644
--- a/modules/merge_and_uncode_rca_uploads.nf
+++ b/modules/merge_and_uncode_rca_uploads.nf
@@ -20,13 +20,13 @@ process merge_and_uncode_rca_uploads {
    if (production) {
       """
       cd /usr/local/src/myscripts/
-      Rscript merge_and_uncode_rca_uploads.R -c $cohort -v --production --save_synapse -c $comment
+      Rscript merge_and_uncode_rca_uploads.R -c $cohort -v --production --save_synapse -cmt $comment
       """
    }
    else {
       """
       cd /usr/local/src/myscripts/
-      Rscript merge_and_uncode_rca_uploads.R -c $cohort -v --save_synapse -c $comment
+      Rscript merge_and_uncode_rca_uploads.R -c $cohort -v --save_synapse -cmt $comment
       """
    }
 }
\ No newline at end of file
diff --git a/scripts/uploads/merge_and_uncode_rca_uploads.R b/scripts/uploads/merge_and_uncode_rca_uploads.R
index 85239a66..a33c1639 100644
--- a/scripts/uploads/merge_and_uncode_rca_uploads.R
+++ b/scripts/uploads/merge_and_uncode_rca_uploads.R
@@ -705,7 +705,7 @@ main <- function(){
                 help="Whether to run in production mode or not (staging mode)."),
     make_option(c("-v", "--verbose"), action="store_true", default = FALSE, 
                 help="Print out verbose output on script progress"),
-    make_option(c("-c", "--comment"), type = "character",
+    make_option(c("-cmt", "--comment"), type = "character",
               help="Comment for new table snapshot version. This must be unique and is tied to the cohort run.")
   )
   opt <- parse_args(OptionParser(option_list=option_list))