Increased fileshare size and separated strategies

process_by_sampleid.sh

@@ -223,7 +223,7 @@ if [[ $exists == "False" ]]; then
         --account-name ${storageAccountResults} \
         --account-key ${storageAccountKeyResults} \
         --name "${shareNameResults}" \
-        --quota 3072 \
+        --quota 9216 \
         --output none
 else
     if [[ $FORCE == 0 ]]; then
@@ -233,10 +233,10 @@ else
         exit 2
     else
         quota=$( az storage share show --account-name ${storageAccountResults} --account-key ${storageAccountKeyResults} --name "${shareNameResults}" --output json --query properties.quota )
-        if [[ $quota < 3072 ]]; then
+        if [[ $quota < 9216 ]]; then
             echo "   [WARNING] File share \"${shareNameResults}\" in \"${storageAccountResults}\""
-            echo "             has a quota smaller than 3072G, resizing to 3072..."
-            az storage share update --account-name ${storageAccountResults} --account-key ${storageAccountKeyResults} --name "${shareNameResults}" --quota 3072
+            echo "             has a quota smaller than 9216G, resizing to 9216..."
+            az storage share update --account-name ${storageAccountResults} --account-key ${storageAccountKeyResults} --name "${shareNameResults}" --quota 9216
         fi
     fi
 fi

wgbs-pipeline.sh

@@ -247,9 +247,6 @@ mkdir -p ${output_dir}
 log_dir=${output_dir}/logs
 mkdir -p ${log_dir}
 
-# Create TMP folder
-tmp_dir=${output_dir}/tmp
-mkdir -p ${tmp_dir}
 
 # Print input data :)
 start_date=$( date )
@@ -308,6 +305,9 @@ else
 fi
 
 if [[ $S1 == "true" ]]; then
+    # Create TMP folder
+    tmp_dir=${output_dir}/tmp_1
+    mkdir -p ${tmp_dir}
     echo "##################################################"
     echo "#                   STRATEGY 1                   #"
     echo "#================================================#"
@@ -476,6 +476,9 @@ fi
 
 
 if [[ $S2 == "true" ]]; then
+    # Create TMP folder
+    tmp_dir=${output_dir}/tmp_2
+    mkdir -p ${tmp_dir}
     echo "##################################################"
     echo "#                   STRATEGY 2                   #"
     echo "#================================================#"
@@ -610,6 +613,9 @@ fi
 
 
 if [[ $S3 == "true" ]]; then
+    # Create TMP folder
+    tmp_dir=${output_dir}/tmp_3
+    mkdir -p ${tmp_dir}
     echo "##################################################"
     echo "#                   STRATEGY 3                   #"
     echo "#================================================#"