Add out dir.

scripts/split_study.sh

@@ -12,7 +12,8 @@ usage() {
   echo "-h  --Help documentation for $script_name"
   echo "-r  --Study_RID."
   echo "-t  --Tag of pipelne"
-  echo "Example: $script_name -r 16-1ZP0 -t 0.1.0"
+  echo "-o  --Path to output directory"
+  echo "Example: $script_name -r 16-1ZP0 -t 0.1.0 -o '/path/to/output/dir/'"
   exit 1
 }
 
@@ -25,11 +26,12 @@ main(){
 
     # Parsing options
     OPTIND=1 # Reset OPTIND
-    while getopts :r:t:h opt
+    while getopts :r:t:0:h opt
         do
             case $opt in
                 r) rid=$OPTARG;;
                 t) tag=$OPTARG;;
+                o) out=$OPTARG;;
                 h) usage;;
             esac
         done
@@ -37,7 +39,7 @@ main(){
     shift $(($OPTIND -1))
 
     # Check for mandatory options
-    if [[ -z $rid ]] || [[ -z $tag ]]; then
+    if [[ -z $rid ]] || [[ -z $tag ]] || [[ -z $out ]]; then
         usage
     fi
 
@@ -52,9 +54,9 @@ main(){
   rm $rid\_studyRID.json
 
   # make dir for study
-  mkdir $rid
-  mv $rid\_studyRID.csv $rid
-  cd $rid
+  mkdir $out/$rid
+  mv $rid\_studyRID.csv $out/$rid
+  cd $out/$rid
 
   # download version of RNA-seq pipelne
   existed_in_remote=$( git ls-remote --tags git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git ${tag})