Added resizing of small results file share

process_by_sampleid.sh

@@ -26,6 +26,11 @@ usage()
     echo "   --strategies STRATEGIES"
     echo "          Only run selected strategies. Possible choices of STRATEGIES: "1", "2", "3""
     echo "          or any combination of them, comma-separated (e.g. "1,2,3", "2,3")."
+    echo "   --shrink-fileshare"
+    echo "          When finished, reduce quota of fileshare to be only 10G more than the total"
+    echo "          space needed for the results. This option is not to be used when other tasks"
+    echo "          are running on the same fileshare (e.g. when running different strategies"
+    echo "          concomitantly."
     echo "   --input-samba-credentials FILE"
     echo "          File with the samba credentials to mount input fileshare (fastqs)."
     echo "   --output-samba-credentials FILE"
@@ -48,6 +53,7 @@ FORCE=0
 MONITOR=0
 SUBSET=0
 STRATEGIES="1,2,3"
+SHRINK=0
 
 smbCredFastq=
 smbCredResults=
@@ -81,6 +87,8 @@ while [ "$1" != "" ]; do
         --strategies )                   shift
                                          STRATEGIES=$1
                                          ;;
+        --shrink-fileshare )             SHRINK=1
+                                         ;;
         -h | --help )                    usage
                                          exit
                                          ;;
@@ -147,6 +155,7 @@ echo "- FORCE: $FORCE"
 echo "- MONITOR: $MONITOR"
 echo "- SUBSET: $SUBSET"
 echo "- STRATEGIES: ${STRATEGIES}"
+echo "- SHRINK: ${SHRINK}"
 echo
 
 echo "ACTUALLY DOING STUFF"
@@ -209,20 +218,32 @@ echo "  *Input FASTQ file share mounted in \"${fastq_folder}\""
 echo ">> Preparing output file share... "
 # Check that results fileshare does NOT exist or issue warning and wait
 exists=$( az storage share exists --account-name ${storageAccountResults} --account-key ${storageAccountKeyResults} --name "${shareNameResults}" --output tsv )
-if [[ $exists == "True" && $FORCE == 0 ]]; then
-    echo "   [ERROR] File share \"${shareNameResults}\" in \"${storageAccountResults}\" ALREADY EXISTS!"
-    echo "           To overwrite, use -f option"
+if [[ $exists == "False" ]]; then
+    az storage share create \
+        --account-name ${storageAccountResults} \
+        --account-key ${storageAccountKeyResults} \
+        --name "${shareNameResults}" \
+        --quota 3072 \
+        --output none
+else
+    if [[ $FORCE == 0 ]]; then
+        echo "   [ERROR] File share \"${shareNameResults}\" in \"${storageAccountResults}\""
+        echo "           ALREADY EXISTS!"
+        echo "           If you don't mind potentially overwriting, use -f option"
+        exit 2
+    else
+        quota=$( az storage share show --account-name ${storageAccountResults} --account-key ${storageAccountKeyResults} --name "${shareNameResults}" --output json --query properties.quota )
+        if [[ $quota < 3072 ]]; then
+            echo "   [WARNING] File share \"${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
+        fi
+    fi
 fi
 
+
 results_folder="/fileshares/${storageAccountResults}/${shareNameResults}"
 
-# Create it
-az storage share create \
-    --account-name ${storageAccountResults} \
-    --account-key ${storageAccountKeyResults} \
-    --name "${shareNameResults}" \
-    --quota 3072 \
-    --output none
 
 sudo mkdir -p ${results_folder}
 
@@ -303,16 +324,22 @@ echo
 echo "**************FINISHED**************"
 echo
 
-# Get space used by files in share in GB
-sleep 30
-size1=$( az storage share stats --name ${shareNameResults} --account-name ${storageAccountResults} --account-key ${storageAccountKeyResults} )
-size2=$( du -sh -BG ${results_folder} | cut -f 1 | tr -d 'G' )
-size=$(( size1 > size2 ? size1 + 10 : size2 + 10))
-
-echo " Output files use around $(( size - 10 )) G"
-echo " Resizing fileshare quota to $size..."
-
-az storage share update --name ${shareNameResults} --account-name ${storageAccountResults} --account-key ${storageAccountKeyResults} --quota ${size}
+# Resize storage file share (CAREFUL IF OTHER TASKS NEED THE SPACE!)
+if [[ $SHRINK > 0 ]]; then
+    echo ">> Shrinking the fileshare..."
+    # Get space used by files in share in GB
+    sleep 30
+    size1=$( az storage share stats --name ${shareNameResults} --account-name ${storageAccountResults} --account-key ${storageAccountKeyResults} )
+    size2=$( du -sh -BG ${results_folder} | cut -f 1 | tr -d 'G' )
+    size=$(( size1 > size2 ? size1 + 10 : size2 + 10))
+    
+    echo " Output files use around $(( size - 10 )) G"
+    echo " Resizing fileshare quota to $size G..."
+    
+    az storage share update --name ${shareNameResults} --account-name ${storageAccountResults} --account-key ${storageAccountKeyResults} --quota ${size}
+else
+    echo "   * Fileshare in storage account left with 3G quota"
+fi
 
 echo 
 cd ~