diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index e6193da..7d130c6 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -40,4 +40,4 @@ jobs:
 
       - name: ShellCheck
         run: |
-          find scripts -name "*.sh" | sort | xargs shellcheck --severity=warning
+          find scripts -name "*.sh" | sort | xargs shellcheck --severity=info
diff --git a/scripts/ANALYSIS.anasum.sh b/scripts/ANALYSIS.anasum.sh
index d3edba0..84be27b 100755
--- a/scripts/ANALYSIS.anasum.sh
+++ b/scripts/ANALYSIS.anasum.sh
@@ -2,7 +2,7 @@
 # script to analyse data files with anasum
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=8:00:00; h_vmem=4000M; tmpdir_size=10G
 
 if [[ $# -lt 3 ]]; then
@@ -37,8 +37,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 FLIST=$1
@@ -55,7 +54,7 @@ if [[ ! -f "$FLIST" ]]; then
 fi
 
 # Check that run parameter file exists
-if [[ "$RUNP" == `basename $RUNP` ]]; then
+if [[ "$RUNP" == $(basename "$RUNP") ]]; then
     RUNP="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/$RUNP"
 fi
 if [[ ! -f "$RUNP" ]]; then
@@ -64,7 +63,7 @@ if [[ ! -f "$RUNP" ]]; then
 fi
 
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/$DATE/ANASUM.ANADATA"
 echo -e "Log files will be written to:\n $LOGDIR"
 mkdir -p "$LOGDIR"
@@ -76,7 +75,7 @@ mkdir -p "$ODIR"
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.anasum_sub"
 
-TIMETAG=`date +"%s"`
+TIMETAG=$(date +"%s")
 
 FSCRIPT="$LOGDIR/ANA.$ONAME-$(date +%s)"
 sed -e "s|FILELIST|$FLIST|" \
@@ -90,13 +89,14 @@ echo "$FSCRIPT.sh"
 
 SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
 # run locally or on cluster (expand shell variables in submission string)
-SUBC=`eval "echo \"$SUBC\""`
+SUBC=$(eval "echo \"$SUBC\"")
 if [[ $SUBC == *"ERROR"* ]]; then
     echo "$SUBC"
     exit
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT.sh`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT".sh)
 
     # account for -terse changing the job number format
     if [[ $SUBC != *-terse* ]] ; then
@@ -106,11 +106,12 @@ if [[ $SUBC == *qsub* ]]; then
     echo "RUN $AFILE JOBID $JOBID"
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-    condor_submit $FSCRIPT.sh.condor
+    condor_submit "$FSCRIPT".sh.condor
 elif [[ $SUBC == *parallel* ]]; then
-    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.$TIMETAG.dat
-    cat $LOGDIR/runscripts.$TIMETAG.dat | $SUBC
+    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts."$TIMETAG".dat
+    # shellcheck disable=SC2086
+    cat "$LOGDIR"/runscripts."$TIMETAG".dat | $SUBC
 
 elif [[ $SUBC == *simple* ]]; then
-	"$FSCRIPT.sh" |& tee $FSCRIPT.log
+	"$FSCRIPT.sh" |& tee "$FSCRIPT".log
 fi
diff --git a/scripts/ANALYSIS.anasum_allcuts.sh b/scripts/ANALYSIS.anasum_allcuts.sh
index 850e8e6..3bf912c 100755
--- a/scripts/ANALYSIS.anasum_allcuts.sh
+++ b/scripts/ANALYSIS.anasum_allcuts.sh
@@ -28,8 +28,8 @@ EPOCH="${3:-V6}"
 IGNORETYPE="IGNOREACCEPTANCE"
 # set this to zero to force reprocessing
 SKIPIFPROCESSED="1"
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFMINORVERSION)
-EDMAJORVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFMINORVERSION)
+EDMAJORVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 # anasum file are writing into this directory
 TMPDIR="$VERITAS_DATA_DIR/tmp/${EDVERSION}/${VERITAS_ANALYSIS_TYPE:0:2}/"
@@ -47,12 +47,12 @@ if [[ ${RUNTYPE} == "PRECUTS" ]]; then
 fi
 
 PREDIR="$VERITAS_PREPROCESSED_DATA_DIR/${VERITAS_ANALYSIS_TYPE:0:2}/mscw/"
-echo $PREDIR
+echo "$PREDIR"
 echo "TMP $TMPDIR"
 
 # temporary file for output
 TMPLOG="$(pwd)/anasum.submit.$(uuidgen).tmp.txt"
-rm -f ${TMPLOG}
+rm -f "${TMPLOG}"
 
 for C in $CUTS
 do
@@ -61,19 +61,19 @@ do
         if  [[ $RUNTYPE == "PRECUTS" ]]; then
             CDIR=$(echo "$CDIR" | sed -E 's/anasum_(NTel[23])([A-Za-z]+)Pre/\1-\2/')
         fi
-        echo $CDIR
+        echo "$CDIR"
         mkdir -p "$TMPDIR/${CDIR}"
-        "$(dirname "$0")/ANALYSIS.anasum_parallel_from_runlist.sh" ${RUNL} \
+        "$(dirname "$0")/ANALYSIS.anasum_parallel_from_runlist.sh" "${RUNL}" \
             "$TMPDIR/${CDIR}" \
-            ${C} \
+            "${C}" \
             ${IGNORETYPE} \
-            $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/ANASUM.runparameter \
-            $PREDIR $SKIPIFPROCESSED | tee -a ${TMPLOG}
+            "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/ANASUM.runparameter \
+            "$PREDIR" $SKIPIFPROCESSED | tee -a "${TMPLOG}"
     elif [[ $RUNTYPE == "V2DL3" ]]; then
         mkdir -p "$TMPDIR/v2dl3_${C}"
-         "$(dirname "$0")/ANALYSIS.v2dl3.sh" ${RUNL} \
+         "$(dirname "$0")/ANALYSIS.v2dl3.sh" "${RUNL}" \
              "$TMPDIR/v2dl3_${C}" \
-             ${C} | tee -a ${TMPLOG}
+             "${C}" | tee -a "${TMPLOG}"
     else
         echo "Error: unknown run type $RUNTYPE (allowed: ANASUM, V2DL3, or PRECUTS)"
         exit
@@ -84,5 +84,5 @@ echo
 echo "===================================================================="
 echo "JOB SUBMISSION"
 echo "===================================================================="
-grep -A 1 "Job submission using HTCondor" ${TMPLOG} | sort -r -u
-rm -f ${TMPLOG}
+grep -A 1 "Job submission using HTCondor" "${TMPLOG}" | sort -r -u
+rm -f "${TMPLOG}"
diff --git a/scripts/ANALYSIS.anasum_combine.sh b/scripts/ANALYSIS.anasum_combine.sh
index c4b196a..60fe9de 100755
--- a/scripts/ANALYSIS.anasum_combine.sh
+++ b/scripts/ANALYSIS.anasum_combine.sh
@@ -2,7 +2,7 @@
 # script to combine anasum files processed in parallel mode
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=0:59:00; h_vmem=12000M; tmpdir_size=150G
 
 if [[ $# -lt 3 ]]; then
@@ -39,9 +39,8 @@ fi
 
 # Run init script
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
-    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
+    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 # Parse command line arguments
 RUNLIST=$1
@@ -57,7 +56,7 @@ if [[ ! -f "$RUNLIST" ]]; then
 fi
 
 # Check that run parameter file exists
-if [[ "$RUNP" == `basename $RUNP` ]]; then
+if [[ "$RUNP" == $(basename "$RUNP") ]]; then
     RUNP="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/$RUNP"
 fi
 if [[ ! -f "$RUNP" ]]; then
@@ -66,7 +65,7 @@ if [[ ! -f "$RUNP" ]]; then
 fi
 
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/ANASUM.COMBINE-${DATE}-$(uuidgen)"
 mkdir -p "$LOGDIR"
 echo -e "Log files will be written to:\n $LOGDIR"
@@ -74,7 +73,7 @@ echo -e "Log files will be written to:\n $LOGDIR"
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.anasum_combine_sub"
 
-FSCRIPT="$LOGDIR/anasum_combine-$DATE-RUN$RUN-$(date +%s)"
+FSCRIPT="$LOGDIR/anasum_combine-$DATE-$(basename "$OUTFILE")-$(date +%s)"
 echo "Run script written to $FSCRIPT"
 
 # Check that anasum output files exist before combining
@@ -94,13 +93,14 @@ chmod u+x "$FSCRIPT.sh"
 
 # run locally or on cluster
 SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-SUBC=`eval "echo \"$SUBC\""`
+SUBC=$(eval "echo \"$SUBC\"")
 if [[ $SUBC == *"ERROR"* ]]; then
     echo "$SUBC"
     exit
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT.sh`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT".sh)
     # account for -terse changing the job number format
     if [[ $SUBC != *-terse* ]] ; then
         echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
@@ -108,15 +108,16 @@ if [[ $SUBC == *qsub* ]]; then
     fi
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-    condor_submit $FSCRIPT.sh.condor
-echo "RUN $RUN JOBID $JOBID"
-    echo "RUN $RUN SCRIPT $FSCRIPT.sh"
+    condor_submit "$FSCRIPT".sh.condor
+echo "OUTFILE $OUTFILE JOBID $JOBID"
+    echo "OUTFILE $OUTFILE SCRIPT $FSCRIPT.sh"
     if [[ $SUBC != */dev/null* ]] ; then
-        echo "RUN $RUN OLOG $FSCRIPT.sh.o$JOBID"
-        echo "RUN $RUN ELOG $FSCRIPT.sh.e$JOBID"
+        echo "OUTFILE $OUTFILE OLOG $FSCRIPT.sh.o$JOBID"
+        echo "OUTFILE $OUTFILE ELOG $FSCRIPT.sh.e$JOBID"
     fi
 elif [[ $SUBC == *sbatch* ]]; then
-    $SUBC $FSCRIPT.sh
+    # shellcheck disable=SC2086
+    $SUBC "$FSCRIPT".sh
 elif [[ $SUBC == *parallel* ]]; then
     echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR/runscripts.$(date +"%s").dat"
 elif [[ "$SUBC" == *simple* ]] ; then
diff --git a/scripts/ANALYSIS.anasum_link_files.sh b/scripts/ANALYSIS.anasum_link_files.sh
index 6cd83b4..720889d 100755
--- a/scripts/ANALYSIS.anasum_link_files.sh
+++ b/scripts/ANALYSIS.anasum_link_files.sh
@@ -25,8 +25,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 RUNLIST=$1
@@ -40,7 +39,7 @@ if [[ ! -f "$RUNLIST" ]]; then
 fi
 
 # output directory
-mkdir -p ${ODIR}
+mkdir -p "${ODIR}"
 # directory schema
 getNumberedDirectory()
 {
@@ -51,17 +50,17 @@ getNumberedDirectory()
     else
         NDIR="${IDIR}/${TRUN:0:2}/"
     fi
-    echo ${NDIR}
+    echo "${NDIR}"
 }
 
-RUNS=`cat "$RUNLIST"`
-NRUNS=`cat "$RUNLIST" | wc -l `
+RUNS=$(cat "$RUNLIST")
+NRUNS=$(cat "$RUNLIST" | wc -l )
 echo "total number of runs to be linked: $NRUNS"
 
 for RUN in "${RUNS[@]}"; do
-    ARCHIVEDIR=$(getNumberedDirectory $RUN $DDIR)
+    ARCHIVEDIR=$(getNumberedDirectory "$RUN" "$DDIR")
     if [ -e "${ARCHIVEDIR}/${RUN}.anasum.root" ]; then
-        ls ${ARCHIVEDIR}/${RUN}.anasum.root
-        ln -f -s ${ARCHIVEDIR}/${RUN}.anasum.root ${ODIR}/${RUN}.anasum.root
+        ls "${ARCHIVEDIR}"/"${RUN}".anasum.root
+        ln -f -s "${ARCHIVEDIR}"/"${RUN}".anasum.root "${ODIR}"/"${RUN}".anasum.root
     fi
 done
diff --git a/scripts/ANALYSIS.anasum_parallel_from_runlist.sh b/scripts/ANALYSIS.anasum_parallel_from_runlist.sh
index 817d6d0..91e4b97 100755
--- a/scripts/ANALYSIS.anasum_parallel_from_runlist.sh
+++ b/scripts/ANALYSIS.anasum_parallel_from_runlist.sh
@@ -2,11 +2,11 @@
 # script to analyse data files with anasum (parallel analysis) from a simple run list
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=0:59:00; h_vmem=4000M; tmpdir_size=1G
 
 # EventDisplay version
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 IRFVERSION="$EDVERSION"
 AUXVERSION="auxv01"
 
@@ -62,9 +62,8 @@ fi
 
 # Run init script
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
-    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
+    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 # Parse command line arguments
 RUNLIST=$1
@@ -84,7 +83,7 @@ if [[ ! -z  $VERITAS_ANALYSIS_TYPE ]]; then
       DISPBDT="0"
    fi
 fi
-echo $VERITAS_ANALYSIS_TYPE $ANATYPE $DISPBDT
+echo "$VERITAS_ANALYSIS_TYPE" "$ANATYPE" $DISPBDT
 
 # short-cuts for gamma/hadron cuts (note: VX to be replaced later in script)
 if [[ $CUTS = "moderate2tel" ]] || [[ $CUTS = "BDTmoderate2tel" ]]; then
@@ -151,12 +150,12 @@ fi
 # remove PointSource and ExtendedSource string from cut file name for radial acceptances names
 if [[ $CUT == *PointSource-* ]] ; then
     CUTRADACC=${CUT/-PointSource-/"-"}
-    echo $CUTRACACC
+    echo "$CUTRADACC"
 elif [[ $CUT == *"Extended"* ]]; then
     CUTRADACC=${CUT/-PointSource-/"-"}
 elif [[ $CUT == *ExtendedSource-* ]]; then
     CUTRADACC=${CUT/-ExtendedSource-/"-"}
-    echo $CUTRADACC
+    echo "$CUTRADACC"
 fi
 
 if [[ $DISPBDT == "1" ]]; then
@@ -201,7 +200,7 @@ NRUNS=$(cat "$RUNLIST" | sort -u | wc -l)
 echo "total number of runs to analyze: $NRUNS"
 
 # Check that run parameter file exists
-if [[ "$RUNP" == `basename $RUNP` ]]; then
+if [[ "$RUNP" == $(basename "$RUNP") ]]; then
     RUNP="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/$RUNP"
 fi
 if [[ ! -f "$RUNP" ]]; then
@@ -210,7 +209,7 @@ if [[ ! -f "$RUNP" ]]; then
 fi
 
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/ANASUM.${CUTS}-${DATE}-$(uuidgen)"
 mkdir -p "$LOGDIR"
 echo -e "Log files will be written to:\n $LOGDIR"
@@ -221,7 +220,7 @@ mkdir -p "$ODIR"
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.anasum_sub"
-TIMETAG=`date +"%s"`
+TIMETAG=$(date +"%s")
 
 # directory schema
 getNumberedDirectory()
@@ -233,7 +232,7 @@ getNumberedDirectory()
     else
         ODIR="${IDIR}/${TRUN:0:2}/"
     fi
-    echo ${ODIR}
+    echo "${ODIR}"
 }
 
 
@@ -243,7 +242,7 @@ for RUN in "${RUNS[@]}"; do
 
     # check if file already has been processed
     if [[ $SKIP == "1" ]]; then
-        ARCHIVEDIR="$(getNumberedDirectory $RUN $VERITAS_PREPROCESSED_DATA_DIR/${VERITAS_ANALYSIS_TYPE:0:2}/anasum_${CUTS})"
+        ARCHIVEDIR="$(getNumberedDirectory "$RUN" "$VERITAS_PREPROCESSED_DATA_DIR"/"${VERITAS_ANALYSIS_TYPE:0:2}"/anasum_"${CUTS}")"
         if [ -e "${ARCHIVEDIR}/${RUN}.anasum.root" ]; then
             echo "$RUN already processed (${ARCHIVEDIR}/${RUN}.anasum.root)"
             echo "skipping run"
@@ -255,14 +254,14 @@ for RUN in "${RUNS[@]}"; do
     TMPINDIR="$INDIR"
     # check for mscw file
     if [ ! -e "$TMPINDIR/$RUN.mscw.root" ]; then
-        TMPINDIR=$(getNumberedDirectory $RUN $INDIR)
+        TMPINDIR=$(getNumberedDirectory "$RUN" "$INDIR")
         if [ ! -e "$TMPINDIR/$RUN.mscw.root" ]; then
             echo "error: mscw file not found: $TMPINDIR/$RUN.mscw.root (also not found in directory above)"
-            touch $ODIR/$RUN.NOTFOUND
+            touch "$ODIR"/"$RUN".NOTFOUND
             continue
         fi
     fi
-    rm -f $ODIR/$RUN.NOTFOUND
+    rm -f "$ODIR"/"$RUN".NOTFOUND
 
     TMPLOGDIR=${LOGDIR}
     # avoid reaching limits of number of files per
@@ -270,9 +269,9 @@ for RUN in "${RUNS[@]}"; do
     if [[ ${NRUNS} -gt 5000 ]]; then
         TMPLOGDIR=${LOGDIR}-${RUN:0:1}
     fi
-    mkdir -p ${TMPLOGDIR}
+    mkdir -p "${TMPLOGDIR}"
     FSCRIPT="$TMPLOGDIR/ANASUM.$RUN-$(date +%s)"
-    rm -f $FSCRIPT.sh
+    rm -f "$FSCRIPT".sh
     echo "Run script written to $FSCRIPT"
 
     sed -e "s|FILELIST|NOTDEFINED|" \
@@ -294,13 +293,14 @@ for RUN in "${RUNS[@]}"; do
 
     # run locally or on cluster
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     if [[ $SUBC == *"ERROR"* ]]; then
         echo "$SUBC"
         exit
     fi
     if [[ $SUBC == *qsub* ]]; then
-        JOBID=`$SUBC $FSCRIPT.sh`
+        # shellcheck disable=SC2086
+        JOBID=$($SUBC "$FSCRIPT".sh)
         # account for -terse changing the job number format
         if [[ $SUBC != *-terse* ]] ; then
             echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
@@ -313,7 +313,8 @@ for RUN in "${RUNS[@]}"; do
         echo "-------------------------------------------------------------------------------"
         echo
 	elif [[ $SUBC == *sbatch* ]]; then
-        $SUBC $FSCRIPT.sh
+        # shellcheck disable=SC2086
+        $SUBC "$FSCRIPT".sh
     elif [[ $SUBC == *parallel* ]]; then
         echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$TMPLOGDIR/runscripts.$TIMETAG.dat"
         echo "RUN $RUN OLOG $FSCRIPT.log"
@@ -324,5 +325,6 @@ done
 
 # Execute all FSCRIPTs locally in parallel
 if [[ $SUBC == *parallel* ]]; then
+    # shellcheck disable=SC2086
     cat "$LOGDIR/runscripts.$TIMETAG.dat" | $SUBC
 fi
diff --git a/scripts/ANALYSIS.dispXGB.sh b/scripts/ANALYSIS.dispXGB.sh
index 48ccd6f..5b44564 100755
--- a/scripts/ANALYSIS.dispXGB.sh
+++ b/scripts/ANALYSIS.dispXGB.sh
@@ -2,7 +2,7 @@
 # XGBoost analysis on mscw data files.
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:59:00; h_vmem=4000M; tmpdir_size=25G
 
 if [ "$#" -lt 3 ]; then
@@ -46,37 +46,37 @@ else
 fi
 
 # make output directory if it doesn't exist
-mkdir -p $ODIR
+mkdir -p "$ODIR"
 echo -e "Output files will be written to:\n $ODIR"
 
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/XGB-${XGB_TYPE}-${DATE}-$(uuidgen)/"
 mkdir -p "$LOGDIR"
 echo -e "Log files will be written to:\n $LOGDIR"
-rm -f ${LOGDIR}/x* 2>/dev/null
+rm -f "${LOGDIR}"/x* 2>/dev/null
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.dispXGB_sub"
-TIMETAG=`date +"%s"`
+TIMETAG=$(date +"%s")
 
 for RUNN in $FILES
 do
     echo "Now analysing run $RUNN"
     FSCRIPT="$LOGDIR/dispXGB-${XGB_TYPE}-$RUNN"
-    rm -f $FSCRIPT.sh
+    rm -f "$FSCRIPT".sh
 
     sed -e "s|RRUN|$RUNN|" \
         -e "s|XXGB|$XGB|" \
         -e "s|XGB_TTYPE|$XGB_TYPE|" \
         -e "s|ANALYSISTYPE|$ANALYSIS_TYPE|" \
-        -e "s|OODIR|$ODIR|" $SUBSCRIPT.sh > $FSCRIPT.sh
+        -e "s|OODIR|$ODIR|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
     chmod u+x "$FSCRIPT.sh"
-    echo $FSCRIPT.sh
+    echo "$FSCRIPT".sh
 
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     if [[ $SUBC == *condor* ]]; then
         "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
         echo
@@ -86,9 +86,10 @@ do
         echo "-------------------------------------------------------------------------------"
         echo
     elif [[ $SUBC == *sbatch* ]]; then
-        $SUBC $FSCRIPT.sh
+        # shellcheck disable=SC2086
+        $SUBC "$FSCRIPT".sh
     elif [[ $SUBC == *parallel* ]]; then
-        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> ${LOGDIR}/runscripts.$TIMETAG.dat
+        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "${LOGDIR}"/runscripts."$TIMETAG".dat
         echo "RUN $RUNN OLOG $FSCRIPT.log"
     elif [[ "$SUBC" == *simple* ]] ; then
        "$FSCRIPT.sh" |& tee "$FSCRIPT.log"
diff --git a/scripts/ANALYSIS.evndisp.sh b/scripts/ANALYSIS.evndisp.sh
index fb6772f..ca786bd 100755
--- a/scripts/ANALYSIS.evndisp.sh
+++ b/scripts/ANALYSIS.evndisp.sh
@@ -2,11 +2,11 @@
 # script to run eventdisplay analysis for VTS data
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:59:00; h_vmem=4000M; tmpdir_size=25G
 
 # EventDisplay version
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 if [ ! -n "$1" ] || [ "$1" = "-h" ]; then
 echo "
@@ -65,9 +65,8 @@ fi
 
 # Run init script
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
-    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
+    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 # create extra stdout for duplication of command output
 # look for ">&5" below
@@ -76,7 +75,7 @@ exec 5>&1
 # Parse command line arguments
 RLIST=$1
 [[ "$2" ]] && ODIR=$2 || ODIR="$VERITAS_USER_DATA_DIR/analysis/Results/$EDVERSION/"
-mkdir -p $ODIR
+mkdir -p "$ODIR"
 
 ACUTS_AUTO="EVNDISP.reconstruction.runparameter.AP.v4x"
 if [[ $VERITAS_ANALYSIS_TYPE = "TS"* ]]; then
@@ -99,6 +98,7 @@ fi
 # VPM is on by default
 VPM=1
 # directory with DB text
+# shellcheck disable=SC2153
 DBTEXTDIRECTORY="${VERITAS_DATA_DIR}/shared/DBTEXT"
 # hardwired alternative data directory
 VERITAS_DATA_DIR_2="/lustre/fs23/group/veritas/data"
@@ -110,13 +110,13 @@ if [ ! -f "$RLIST" ] ; then
     echo "Error, runlist $RLIST not found, exiting..."
     exit 1
 fi
-FILES=`cat "$RLIST"`
+FILES=$(cat "$RLIST")
 
-NRUNS=`cat "$RLIST" | wc -l `
+NRUNS=$(cat "$RLIST" | wc -l )
 echo "total number of runs to analyze: $NRUNS"
 echo
 # run scripts are written into this directory
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/EVN.${DATE}-$(uuidgen)/"
 mkdir -p "$LOGDIR"
 echo -e "Log files will be written to:\n $LOGDIR"
@@ -125,10 +125,10 @@ echo -e "Log files will be written to:\n $LOGDIR"
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.evndisp_sub"
 # run locally or on cluster
 SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-SUBC=`eval "echo \"$SUBC\""`
+SUBC=$(eval "echo \"$SUBC\"")
 
 if [[ $SUBC == *parallel* ]]; then
-   touch $LOGDIR/runscripts.sh
+   touch "$LOGDIR"/runscripts.sh
 fi
 
 echo "total number of runs to analyze: $NRUNS"
@@ -146,11 +146,11 @@ fi
 # low gain calibration file
 for T in Tel_1 Tel_2 Tel_3 Tel_4
 do
-    mkdir -p ${ODIR}/Calibration/${T}
+    mkdir -p "${ODIR}"/Calibration/${T}
 done
 if [[ -e "${VERITAS_EVNDISP_AUX_DIR}/Calibration/calibrationlist.LowGain.dat" ]]; then
    if [[ ! -e ${ODIR}/Calibration/calibrationlist.LowGain.dat ]]; then
-       cp -f -v ${VERITAS_EVNDISP_AUX_DIR}/Calibration/calibrationlist.LowGain.dat ${ODIR}/Calibration/
+       cp -f -v "${VERITAS_EVNDISP_AUX_DIR}"/Calibration/calibrationlist.LowGain.dat "${ODIR}"/Calibration/
    fi
 else
    echo "error - low-gain calibration list not found (${VERITAS_EVNDISP_AUX_DIR}/Calibration/calibrationlist.LowGain.dat)"
@@ -158,7 +158,7 @@ else
 fi
 if [[ -e "${VERITAS_EVNDISP_AUX_DIR}/Calibration/LowGainPedestals.lped" ]]; then
    if [[ ! -e ${ODIR}/Calibration/LowGainPedestals.lped ]]; then
-       cp -f -v ${VERITAS_EVNDISP_AUX_DIR}/Calibration/LowGainPedestals.lped ${ODIR}/Calibration/
+       cp -f -v "${VERITAS_EVNDISP_AUX_DIR}"/Calibration/LowGainPedestals.lped "${ODIR}"/Calibration/
    fi
 else
    echo "error - low-gain calibration list not found (${VERITAS_EVNDISP_AUX_DIR}/Calibration/LowGainPedestals.lped)"
@@ -192,7 +192,7 @@ do
 
     # check if file is on disk
     if [[ $SKIP == "1" ]]; then
-        FDISK=$(file_on_disk $FILE)
+        FDISK=$(file_on_disk "$FILE")
         if [[ $FDISK == "TRUE" ]]; then
             echo "RUN $FILE already processed; skipping"
             continue
@@ -253,7 +253,8 @@ do
     fi
 
     if [[ $SUBC == *qsub* ]]; then
-        JOBID=`$SUBC $FSCRIPT.sh`
+        # shellcheck disable=SC2086
+        JOBID=$($SUBC "$FSCRIPT".sh)
         # account for -terse changing the job number format
         if [[ $SUBC != *-terse* ]] ; then
             echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
@@ -275,9 +276,10 @@ do
         echo "-------------------------------------------------------------------------------"
         echo
     elif [[ $SUBC == *sbatch* ]]; then
-        $SUBC $FSCRIPT.sh
+        # shellcheck disable=SC2086
+        $SUBC "$FSCRIPT".sh
     elif [[ $SUBC == *parallel* ]]; then
-        echo "$FSCRIPT.sh" >> $LOGDIR/runscripts.sh
+        echo "$FSCRIPT.sh" >> "$LOGDIR"/runscripts.sh
         echo "RUN $FILE OLOG $FSCRIPT.log"
     elif [[ "$SUBC" == *simple* ]] ; then
         "$FSCRIPT.sh" | tee "$FSCRIPT.log"
@@ -296,12 +298,16 @@ if [[ $SUBC == *parallel* ]]; then
     echo
     echo "$LOGDIR/runscripts.sh"
     echo
-    chmod +x $LOGDIR/runscripts.sh
-    echo "echo \"==================================\"" >> Run_me.sh
-    echo "echo \"List of scripts to run\"" >> Run_me.sh
-    cat $LOGDIR/runscripts.sh | sort -u | awk "{print \$1}" | sed 's/.*/echo \" & \"/' >> Run_me.sh
-    echo "cat $LOGDIR/runscripts.sh | sort -u | $SUBC" >> Run_me.sh
+    chmod +x "$LOGDIR"/runscripts.sh
+    {
+        echo "echo \"==================================\""
+        echo "echo \"List of scripts to run\""
+        cat "$LOGDIR"/runscripts.sh | sort -u | awk "{print \$1}" | sed 's/.*/echo \" & \"/'
+        # shellcheck disable=SC2086
+        echo "cat $LOGDIR/runscripts.sh | sort -u | $SUBC"
+    } >> Run_me.sh
     chmod +x Run_me.sh
+# shellcheck source=/dev/null
     source Run_me.sh
     rm Run_me.sh
 fi
diff --git a/scripts/ANALYSIS.evndisp_laser.sh b/scripts/ANALYSIS.evndisp_laser.sh
index 51ccf2f..c5cb6ff 100755
--- a/scripts/ANALYSIS.evndisp_laser.sh
+++ b/scripts/ANALYSIS.evndisp_laser.sh
@@ -2,7 +2,7 @@
 # script run eventdisplay laser analysis with a queue system
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:29:00; h_vmem=2000M; tmpdir_size=5G
 
 if [ ! -n "$1" ] || [ "$1" = "-h" ]; then
@@ -33,8 +33,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 CDIR=$(dirname "$0")
 
 # Parse command line arguments
@@ -47,15 +46,15 @@ if [[ ! -f "$RLIST" ]] ; then
     echo "Error, runlist $RLIST not found, exiting..."
     exit 1
 fi
-RUNNUMS=`cat $RLIST`
+RUNNUMS=$(cat "$RLIST")
 echo "Laser files to analyze:"
-echo $RUNNUMS
+echo "$RUNNUMS"
 
 # Output directory for error/output from batch system
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/$DATE/EVNDISP.ANADATA"
 echo "Log files will be written to: $LOGDIR"
-mkdir -p $LOGDIR
+mkdir -p "$LOGDIR"
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.evndisp_laser_sub"
@@ -64,7 +63,7 @@ SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.evndisp_laser_sub"
 # loop over all files in files loop
 for RUN in $RUNNUMS; do
     # check if laser file exists
-    #DFILE=`find -L $VERITAS_DATA_DIR/data/ -name "$RUN.cvbf"`
+    #DFILE=$(find -L $VERITAS_DATA_DIR/data/ -name "$RUN.cvbf")
     #if [ -z "$DFILE" ]; then
     #    echo "Error: laser vbf file not found for run $RUN"
     #    continue
@@ -83,16 +82,17 @@ for RUN in $RUNNUMS; do
     sed -e "s|RUNFILE|$RUN|" \
         -e "s|TELTOANACOMB|$TELTOANA|" \
         -e "s|CURRENTDIR|$CDIR|" \
-        -e "s|LOGDIRECTORY|$LOGDIR|" $SUBSCRIPT.sh > $FSCRIPT.sh
+        -e "s|LOGDIRECTORY|$LOGDIR|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
-    chmod u+x $FSCRIPT.sh
-    echo $FSCRIPT.sh
+    chmod u+x "$FSCRIPT".sh
+    echo "$FSCRIPT".sh
 
     # run locally or on cluster
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     if [[ $SUBC == *qsub* ]]; then
-        JOBID=`$SUBC $FSCRIPT.sh`
+        # shellcheck disable=SC2086
+        JOBID=$($SUBC "$FSCRIPT".sh)
 
         # account for -terse changing the job number format
         if [[ $SUBC != *-terse* ]] ; then
@@ -103,11 +103,12 @@ for RUN in $RUNNUMS; do
         echo "RUN $RUN: JOBID $JOBID"
     elif [[ $SUBC == *condor* ]]; then
         "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-        condor_submit $FSCRIPT.sh.condor
+        condor_submit "$FSCRIPT".sh.condor
     elif [[ $SUBC == *sbatch* ]]; then
-        $SUBC $FSCRIPT.sh
+        # shellcheck disable=SC2086
+        $SUBC "$FSCRIPT".sh
     elif [[ $SUBC == *parallel* ]]; then
-        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.dat
+        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts.dat
     elif [[ "$SUBC" == *simple* ]] ; then
         "$FSCRIPT.sh" |& tee "$FSCRIPT.log"
     fi
@@ -115,7 +116,8 @@ done
 
 # Execute all FSCRIPTs locally in parallel
 if [[ $SUBC == *parallel* ]]; then
-    cat $LOGDIR/runscripts.dat | $SUBC
+    # shellcheck disable=SC2086
+    cat "$LOGDIR"/runscripts.dat | $SUBC
 fi
 
 exit
diff --git a/scripts/ANALYSIS.evndisp_muon.sh b/scripts/ANALYSIS.evndisp_muon.sh
index f12ea82..30b242e 100755
--- a/scripts/ANALYSIS.evndisp_muon.sh
+++ b/scripts/ANALYSIS.evndisp_muon.sh
@@ -2,11 +2,11 @@
 # script to run eventdisplay analysis for VTS data
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:59:00; h_vmem=2000M; tmpdir_size=25G
 
 # EventDisplay version
-EDVERSION=`$EVNDISPSYS/bin/evndisp --version | tr -d .`
+EDVERSION=$("$EVNDISPSYS"/bin/evndisp --version | tr -d .)
 
 if [ ! -n "$1" ] || [ "$1" = "-h" ]; then
 # begin help message
@@ -66,8 +66,7 @@ exit
 fi
 
 # Run init script
-bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # create extra stdout for duplication of command output
 # look for ">&5" below
@@ -76,7 +75,7 @@ exec 5>&1
 # Parse command line arguments
 RLIST=$1
 [[ "$2" ]] && ODIR=$2 || ODIR="$VERITAS_USER_DATA_DIR/analysis/Results/$EDVERSION/"
-mkdir -p $ODIR
+mkdir -p "$ODIR"
 
 # Try to use the correct reconstruction runparameters. For V4 and V5 the default is GRISU / SumWindow6-noDISP.
 if [[ "$SIMTYPE" == "CARE"* ]]; then
@@ -109,19 +108,19 @@ if [ ! -f "$RLIST" ] ; then
     echo "Error, runlist $RLIST not found, exiting..."
     exit 1
 fi
-FILES=`cat $RLIST`
+FILES=$(cat "$RLIST")
 
 # Output directory for error/output
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/$DATE/EVNDISP.ANADATA"
-mkdir -p $LOGDIR
+mkdir -p "$LOGDIR"
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.evndisp_sub"
 
-TIMETAG=`date +"%s"`
+TIMETAG=$(date +"%s")
 
-NRUNS=`cat $RLIST | wc -l `
+NRUNS=$(cat "$RLIST" | wc -l )
 echo "total number of runs to analyze: $NRUNS"
 echo
 
@@ -140,10 +139,10 @@ do
         -e "s|TELTOANACOMB|$TELTOANA|"                   \
         -e "s|USECALIBLIST|$CALIBFILE|"                  \
         -e "s|USEMODEL3D|$MODEL3D|"                      \
-        -e "s|EXTRAPARS|\"$EXTRAPARS\"|" $SUBSCRIPT.sh > $FSCRIPT.sh
+        -e "s|EXTRAPARS|\"$EXTRAPARS\"|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
-    chmod u+x $FSCRIPT.sh
-    echo $FSCRIPT.sh
+    chmod u+x "$FSCRIPT".sh
+    echo "$FSCRIPT".sh
 	# output selected input during submission:
 
 	echo "Using runparameter file $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/$ACUTS"
@@ -171,9 +170,10 @@ do
 
     # run locally or on cluster
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     if [[ $SUBC == *qsub* ]]; then
-        JOBID=`$SUBC $FSCRIPT.sh`
+        # shellcheck disable=SC2086
+        JOBID=$($SUBC "$FSCRIPT".sh)
         # account for -terse changing the job number format
         if [[ $SUBC != *-terse* ]] ; then
             echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
@@ -188,11 +188,12 @@ do
         fi
     elif [[ $SUBC == *condor* ]]; then
         "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-        condor_submit $FSCRIPT.sh.condor
+        condor_submit "$FSCRIPT".sh.condor
     elif [[ $SUBC == *sbatch* ]]; then
-        $SUBC $FSCRIPT.sh
+        # shellcheck disable=SC2086
+        $SUBC "$FSCRIPT".sh
     elif [[ $SUBC == *parallel* ]]; then
-        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.$TIMETAG.dat
+        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts."$TIMETAG".dat
         echo "RUN $AFILE OLOG $FSCRIPT.log"
     elif [[ "$SUBC" == *simple* ]] ; then
 	"$FSCRIPT.sh" |& tee "$FSCRIPT.log"
@@ -201,7 +202,8 @@ done
 
 # Execute all FSCRIPTs locally in parallel
 if [[ $SUBC == *parallel* ]]; then
-    cat $LOGDIR/runscripts.$TIMETAG.dat | sort -u | $SUBC
+    # shellcheck disable=SC2086
+    cat "$LOGDIR"/runscripts."$TIMETAG".dat | sort -u | $SUBC
 fi
 
 exit
diff --git a/scripts/ANALYSIS.mscw_energy.sh b/scripts/ANALYSIS.mscw_energy.sh
index e8d19d4..c0f1272 100755
--- a/scripts/ANALYSIS.mscw_energy.sh
+++ b/scripts/ANALYSIS.mscw_energy.sh
@@ -2,11 +2,11 @@
 # script to analyse data files with lookup tables
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=00:29:00; h_vmem=4000M; tmpdir_size=4G
 
 # EventDisplay version
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 IRFVERSION="$EDVERSION"
 
 if [ "$#" -lt 2 ]; then
@@ -44,9 +44,8 @@ fi
 
 # Run init script
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
-    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
+    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 # create extra stdout for duplication of command output
 # look for ">&5" below
@@ -71,18 +70,18 @@ NRUNS=$(cat "$RUNLIST" | wc -l)
 echo "total number of runs to analyze: $NRUNS"
 
 # make output directory if it doesn't exist
-mkdir -p $ODIR
+mkdir -p "$ODIR"
 echo -e "Output files will be written to:\n $ODIR"
 
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/MSCW.${DATE}-$(uuidgen)/"
 mkdir -p "$LOGDIR"
 echo -e "Log files will be written to:\n $LOGDIR"
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.mscw_energy_sub"
-TIMETAG=`date +"%s"`
+TIMETAG=$(date +"%s")
 
 # directory schema
 getNumberedDirectory()
@@ -94,7 +93,7 @@ getNumberedDirectory()
     else
         ODIR="${IDIR}/${TRUN:0:2}/"
     fi
-    echo ${ODIR}
+    echo "${ODIR}"
 }
 
 
@@ -109,7 +108,7 @@ do
     if [[ $SKIP == "1" ]]; then
         TMPDIR="$VERITAS_PREPROCESSED_DATA_DIR/${VERITAS_ANALYSIS_TYPE:0:2}/mscw/"
         if [[ -d "$TMPDIR" ]]; then
-            TMPMDIR=$(getNumberedDirectory $RUNN "$TMPDIR")
+            TMPMDIR=$(getNumberedDirectory "$RUNN" "$TMPDIR")
             if [ -e "$TMPMDIR/$RUNN.mscw.root" ]; then
                 echo "RUN $RUNN already processed; skipping (FOUND IN $TMPMDIR/$RUNN.mscw.root)"
                 continue
@@ -120,7 +119,7 @@ do
 
     # EVNDISP file
     if [ ! -e "$BFILE" ]; then
-        TMPINDIR=$(getNumberedDirectory $RUNN ${INPUTDIR})
+        TMPINDIR=$(getNumberedDirectory "$RUNN" "${INPUTDIR}")
         if [ ! -e "$TMPINDIR/$RUNN.root" ]; then
             echo "ERR: File $BFILE does not exist" >> mscw.errors.log
             continue
@@ -134,26 +133,27 @@ do
     # directory (e.g., on afs)
     if [[ ${NRUNS} -gt 1000 ]]; then
         TMPLOGDIR=${LOGDIR}/MSCW_${RUNN:0:1}
-        mkdir -p ${TMPLOGDIR}
+        mkdir -p "${TMPLOGDIR}"
     fi
     FSCRIPT="$TMPLOGDIR/MSCW.data-ID$ID-$RUNN"
-    rm -f $FSCRIPT.sh
+    rm -f "$FSCRIPT".sh
 
     sed -e "s|RECONSTRUCTIONID|$ID|" \
         -e "s|OUTPUTDIRECTORY|$ODIR|" \
         -e "s|BDTDISP|${DISPBDT}|" \
         -e "s|VERSIONIRF|${IRFVERSION}|" \
-        -e "s|EVNDISPFILE|$BFILE|" $SUBSCRIPT.sh > $FSCRIPT.sh
+        -e "s|EVNDISPFILE|$BFILE|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
     chmod u+x "$FSCRIPT.sh"
-    echo $FSCRIPT.sh
+    echo "$FSCRIPT".sh
 
     # run locally or on cluster
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     echo "Submission command: $SUBC"
     if [[ $SUBC == *qsub* ]]; then
-        JOBID=`$SUBC $FSCRIPT.sh`
+        # shellcheck disable=SC2086
+        JOBID=$($SUBC "$FSCRIPT".sh)
         # account for -terse changing the job number format
         if [[ $SUBC != *-terse* ]] ; then
             echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
@@ -175,9 +175,10 @@ do
         echo "-------------------------------------------------------------------------------"
         echo
     elif [[ $SUBC == *sbatch* ]]; then
-        $SUBC $FSCRIPT.sh
+        # shellcheck disable=SC2086
+        $SUBC "$FSCRIPT".sh
     elif [[ $SUBC == *parallel* ]]; then
-        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> ${TMPLOGDIR}/runscripts.$TIMETAG.dat
+        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "${TMPLOGDIR}"/runscripts."$TIMETAG".dat
         echo "RUN $RUNN OLOG $FSCRIPT.log"
     elif [[ "$SUBC" == *simple* ]] ; then
         "$FSCRIPT.sh" |& tee "$FSCRIPT.log"
@@ -186,7 +187,8 @@ done
 
 # Execute all FSCRIPTs locally in parallel
 if [[ $SUBC == *parallel* ]]; then
-    cat $TMPLOGDIR/runscripts.$TIMETAG.dat | $SUBC
+    # shellcheck disable=SC2086
+    cat "$TMPLOGDIR"/runscripts."$TIMETAG".dat | $SUBC
 fi
 
 echo "LOG/SUBMIT DIR: ${TMPLOGDIR}"
diff --git a/scripts/ANALYSIS.v2dl3.sh b/scripts/ANALYSIS.v2dl3.sh
index 9d6b247..de13df8 100755
--- a/scripts/ANALYSIS.v2dl3.sh
+++ b/scripts/ANALYSIS.v2dl3.sh
@@ -5,7 +5,7 @@
 #
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:59:00; h_vmem=4000M; tmpdir_size=25G
 
 if [ "$#" -lt 3 ]; then
@@ -47,52 +47,53 @@ echo "total number of runs to analyze: $NRUNS"
 echo
 
 # make output directory if it doesn't exist
-mkdir -p $ODIR
+mkdir -p "$ODIR"
 echo -e "Output files will be written to:\n $ODIR"
 
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/V2DL3-${DATE}-$(uuidgen)/"
 mkdir -p "$LOGDIR"
 echo -e "Log files will be written to:\n $LOGDIR"
-rm -f ${LOGDIR}/x* 2>/dev/null
+rm -f "${LOGDIR}"/x* 2>/dev/null
 
 # split run list into smaller run lists
 sort -u "${RUNLIST}" -o "${LOGDIR}/$(basename "${RUNLIST}")"
-(cd "${LOGDIR}" && split -l $SPLITRUN "${LOGDIR}/$(basename ${RUNLIST})")
+(cd "${LOGDIR}" && split -l "$SPLITRUN" "${LOGDIR}/$(basename "${RUNLIST}")")
 
-FILELISTS=$(ls ${LOGDIR}/x*)
-NFILELISTS=$(ls ${LOGDIR}/x* | wc -l)
+FILELISTS=$(find "$LOGDIR" -maxdepth 1 -name "x*" | sort)
+NFILELISTS=$(find "$LOGDIR" -maxdepth 1 -name "x*" | wc -l)
 
 echo -e "Processing $NFILELISTS file lists (equal to number of jobs)"
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.v2dl3_sub"
-TIMETAG=`date +"%s"`
+TIMETAG=$(date +"%s")
 
 for J in ${FILELISTS}
 do
     echo "Submitting analysis for file list $J"
 
-    FSCRIPT="$LOGDIR/V2DL3-$(basename $J)"
-    rm -f $FSCRIPT.sh
+    FSCRIPT="$LOGDIR/V2DL3-$(basename "$J")"
+    rm -f "$FSCRIPT".sh
     echo "Run script written to $FSCRIPT"
 
     sed -e "s|RRUNLIST|$J|" \
         -e "s|OODIR|$ODIR|" \
-        -e "s|CCUT|$CUT|" $SUBSCRIPT.sh > $FSCRIPT.sh
+        -e "s|CCUT|$CUT|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
     chmod u+x "$FSCRIPT.sh"
 
     # run locally or on cluster
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     if [[ $SUBC == *"ERROR"* ]]; then
         echo "$SUBC"
         exit
     fi
     if [[ $SUBC == *qsub* ]]; then
-        JOBID=`$SUBC $FSCRIPT.sh`
+        # shellcheck disable=SC2086
+        JOBID=$($SUBC "$FSCRIPT".sh)
         # account for -terse changing the job number format
         if [[ $SUBC != *-terse* ]] ; then
             echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
@@ -114,7 +115,8 @@ do
         echo "-------------------------------------------------------------------------------"
         echo
 	elif [[ $SUBC == *sbatch* ]]; then
-        $SUBC $FSCRIPT.sh
+        # shellcheck disable=SC2086
+        $SUBC "$FSCRIPT".sh
     elif [[ $SUBC == *parallel* ]]; then
         echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR/runscripts.$TIMETAG.dat"
         echo "RUN $J OLOG $FSCRIPT.log"
@@ -125,5 +127,6 @@ done
 
 # Execute all FSCRIPTs locally in parallel
 if [[ $SUBC == *parallel* ]]; then
+    # shellcheck disable=SC2086
     cat "$LOGDIR/runscripts.$TIMETAG.dat" | $SUBC
 fi
diff --git a/scripts/IRF.combine_effective_area_parts.sh b/scripts/IRF.combine_effective_area_parts.sh
index 04ffaec..46bab66 100755
--- a/scripts/IRF.combine_effective_area_parts.sh
+++ b/scripts/IRF.combine_effective_area_parts.sh
@@ -2,11 +2,11 @@
 # combine effective area files into one
 
 # job requirements
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:29:00; h_vmem=12000M; tmpdir_size=20G
 #
 # EventDisplay version
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 if [ $# -lt 5 ]; then
 echo "
@@ -45,9 +45,8 @@ fi
 
 # Run init script
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 # date used in run scripts / log file directories
 DATE=$(date +"%y%m%d")
@@ -64,7 +63,7 @@ SIMTYPE=$5
 [[ "${9}" ]] && UUID=${9} || UUID=${DATE}-$(uuidgen)
 
 # Generate EA base file name based on cuts file
-CUTS_NAME=`basename $CUTSFILE`
+CUTS_NAME=$(basename "$CUTSFILE")
 CUTS_NAME=${CUTS_NAME##ANASUM.GammaHadron-}
 CUTS_NAME=${CUTS_NAME%%.dat}
 
@@ -128,24 +127,25 @@ SUBSCRIPT="$(dirname "$0")/helper_scripts/IRF.effective_area_combine_sub"
 
 # make run script
 FSCRIPT="$LOGDIR/COMB-EFFAREA-ID${RECID}-${CUTS_NAME}-ATM${ATMOS}-${EPOCH}-${DISPBDT}-$(date +%s%N)"
-rm -f $FSCRIPT.sh
+rm -f "$FSCRIPT".sh
 
 sed -e "s|INPUTFILES|$INFILES|" \
     -e "s|OUTPUTFILE|$OFILE|"   \
-    -e "s|OUTPUTDIR|$ODIR|" $SUBSCRIPT.sh > $FSCRIPT.sh
+    -e "s|OUTPUTDIR|$ODIR|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
 chmod u+x "$FSCRIPT.sh"
 echo "Run script written to: $FSCRIPT"
 
 # run locally or on cluster
 SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-SUBC=`eval "echo \"$SUBC\""`
+SUBC=$(eval "echo \"$SUBC\"")
 if [[ $SUBC == *"ERROR"* ]]; then
     echo "$SUBC"
     exit
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT.sh`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT".sh)
     echo "JOBID: $JOBID"
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
@@ -156,7 +156,8 @@ elif [[ $SUBC == *condor* ]]; then
     echo "-------------------------------------------------------------------------------"
     echo
 elif [[ $SUBC == *sbatch* ]]; then
-    $SUBC $FSCRIPT.sh
+    # shellcheck disable=SC2086
+    $SUBC "$FSCRIPT".sh
 elif [[ $SUBC == *parallel* ]]; then
     echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR/runscripts.dat"
 elif [[ "$SUBC" == *simple* ]]; then
diff --git a/scripts/IRF.combine_lookup_table_parts.sh b/scripts/IRF.combine_lookup_table_parts.sh
index d4ceaac..92876b0 100755
--- a/scripts/IRF.combine_lookup_table_parts.sh
+++ b/scripts/IRF.combine_lookup_table_parts.sh
@@ -2,11 +2,11 @@
 # script to combine several table file into one
 
 # job requirements
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=20:29:00; h_vmem=12000M; tmpdir_size=10G
 
 # EventDisplay version
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 if [ $# -lt 4 ]; then
 echo "
@@ -40,9 +40,8 @@ fi
 
 # Run init script
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 # date used in run scripts / log file directories
 DATE=$(date +"%y%m%d")
@@ -88,8 +87,8 @@ mkdir -p "$LOGDIR"
 # Create list of partial table files
 FLIST=$OFILE.list
 rm -f "$ODIR/$FLIST"
-ls -1 $INDIR/*ID${RECID}.root > "$ODIR/$FLIST"
-NFIL=`cat "$ODIR/$FLIST" | wc -l`
+ls -1 "$INDIR"/*ID"${RECID}".root > "$ODIR/$FLIST"
+NFIL=$(cat "$ODIR/$FLIST" | wc -l)
 if [[ $NFIL = "0" ]]; then
    echo "No lookup table root files found"
    exit
@@ -105,20 +104,21 @@ FSCRIPT="$LOGDIR/TABLES-COMBINE.$OFILE.$DATE.MC"
 
 sed -e "s|TABLELIST|$FLIST|" \
     -e "s|OUTPUTFILE|$OFILE|" \
-    -e "s|OUTPUTDIR|$ODIR|" $SUBSCRIPT.sh > $FSCRIPT.sh
+    -e "s|OUTPUTDIR|$ODIR|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
 chmod u+x "$FSCRIPT.sh"
 echo "Run script written to: $FSCRIPT"
 
 # run locally or on cluster
 SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-SUBC=`eval "echo \"$SUBC\""`
+SUBC=$(eval "echo \"$SUBC\"")
 if [[ $SUBC == *"ERROR"* ]]; then
     echo "$SUBC"
     exit
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT.sh`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT".sh)
     echo "JOBID: $JOBID"
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
@@ -129,6 +129,6 @@ elif [[ $SUBC == *condor* ]]; then
     echo "-------------------------------------------------------------------------------"
     echo
 elif [[ $SUBC == *parallel* ]]; then
-    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.dat
+    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts.dat
 fi
 echo "LOG/SUBMIT DIR: ${LOGDIR}"
diff --git a/scripts/IRF.compress_evndisp_MC.sh b/scripts/IRF.compress_evndisp_MC.sh
index e581299..9dfa8fa 100755
--- a/scripts/IRF.compress_evndisp_MC.sh
+++ b/scripts/IRF.compress_evndisp_MC.sh
@@ -3,7 +3,7 @@
 #
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=0:29:00; h_vmem=4000M; tmpdir_size=20G
 
 if [ $# -lt 7 ]; then
@@ -48,13 +48,12 @@ exit
 fi
 
 # Run init script
-bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # EventDisplay version
-EDVERSION=`$EVNDISPSYS/bin/evndisp --version | tr -d .`
+EDVERSION=$("$EVNDISPSYS"/bin/evndisp --version | tr -d .)
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 
 # Parse command line arguments
 SIMDIR=$1
@@ -86,24 +85,18 @@ LOGDIR="${VERITAS_IRFPRODUCTION_DIR}/$EDVERSION/${ANALYSIS_TYPE}/${SIMTYPE}/${EP
 mkdir -p "$LOGDIR"
 echo -e "input files will be read from:\n $IPDIR"
 
-# Analysis options
-EDOPTIONS=""
-if [[ ${ANALYSIS_TYPE} == *"SQ2"* ]]; then
-   EDOPTIONS="-imagesquared"
-fi
-
 # Create a unique set of run numbers
 if [[ ${SIMTYPE:0:5} = "GRISU" ]]; then
     [[ ${EPOCH:0:2} == "V4" ]] && RUNNUM="946500"
     [[ ${EPOCH:0:2} == "V5" ]] && RUNNUM="956500"
     [[ ${EPOCH:0:2} == "V6" ]] && RUNNUM="966500"
-elif [ ${SIMTYPE:0:4} = "CARE" ]; then
+elif [ "${SIMTYPE:0:4}" = "CARE" ]; then
     [[ ${EPOCH:0:2} == "V4" ]] && RUNNUM="941200"
     [[ ${EPOCH:0:2} == "V5" ]] && RUNNUM="951200"
     [[ ${EPOCH:0:2} == "V6" ]] && RUNNUM="961200"
 fi
 
-INT_WOBBLE=`echo "$WOBBLE*100" | bc | awk -F '.' '{print $1}'`
+INT_WOBBLE=$(echo "$WOBBLE*100" | bc | awk -F '.' '{print $1}')
 if [[ ${#INT_WOBBLE} -lt 2 ]]; then
    INT_WOBBLE="000"
 elif [[ ${#INT_WOBBLE} -lt 3 ]]; then
@@ -120,68 +113,65 @@ NOISEFILE="NO_NOISEFILE"
 #######################################################
 # GRISU simulations
 if [[ ${SIMTYPE:0:5} == "GRISU" ]]; then
-    if [[ -z $VERITAS_EVNDISP_AUX_DIR ]]; then
-        VERITAS_EVNDISP_AUX_DIR=$VERITAS_EVNDISP_AUX_DIR
-    fi
     # Input files (observe that these might need some adjustments)
     if [[ ${EPOCH:0:2} == "V4" ]]; then
         if [[ $ATM == "21" ]]; then
-            VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "Oct2012_oa_ATM21_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
+            VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "Oct2012_oa_ATM21_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
         else
-            VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "gamma_V4_Oct2012_SummerV4ForProcessing_20130611_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
+            VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "gamma_V4_Oct2012_SummerV4ForProcessing_20130611_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
         fi
         NOISEFILE="$VERITAS_EVNDISP_AUX_DIR/NOISE/NOISE$NOISE.grisu"
     elif [[ ${EPOCH:0:2} == "V5" ]]; then
-        VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "gamma_V5_Oct2012_newArrayConfig_20121027_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
+        VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "gamma_V5_Oct2012_newArrayConfig_20121027_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
         NOISEFILE="$VERITAS_EVNDISP_AUX_DIR/NOISE/NOISE$NOISE.grisu"
     elif [[ ${EPOCH:0:2} == "V6" ]]; then
         if [[ $ATM == "21-redHV" ]]; then
-            VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "gamma_V6_Upgrade_ReducedHV_20121211_v420_ATM21_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
+            VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "gamma_V6_Upgrade_ReducedHV_20121211_v420_ATM21_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
         elif [[ $ATM == "21-UV" ]]; then
-            VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "gamma_V6_Upgrade_UVfilters_20121211_v420_ATM21_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
+            VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "gamma_V6_Upgrade_UVfilters_20121211_v420_ATM21_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
         elif [[ $ATM == "21-SNR" ]]; then
-            VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "gamma_V6_201304_SN2013ak_v420_ATM21_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
+            VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "gamma_V6_201304_SN2013ak_v420_ATM21_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
         else
-            VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "gamma_V6_Upgrade_20121127_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
+            VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "gamma_V6_Upgrade_20121127_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*" -not -name "*.log" -not -name "*.md5sum")
         fi
         NOISEFILE="$VERITAS_EVNDISP_AUX_DIR/NOISE/NOISE${NOISE}_20120827_v420.grisu"
     fi
 #######################################################
-elif [ ${SIMTYPE} == "CARE_UV_June1409" ]; then
+elif [ "${SIMTYPE}" == "CARE_UV_June1409" ]; then
     # example gamma_00deg_750m_0.5wob_180mhz_up_ATM21_part0.cvbf.bz2
-    WOFFSET=$(awk -v WB=$WOBBLE 'BEGIN { printf("%03d",100*WB) }')
-    VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "gamma_${ZA}deg_750m_${WOBBLE}wob_${NOISE}mhz_up_ATM${ATM}_part0.cvbf.bz2")
+    WOFFSET=$(awk -v WB="$WOBBLE" 'BEGIN { printf("%03d",100*WB) }')
+    VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "gamma_${ZA}deg_750m_${WOBBLE}wob_${NOISE}mhz_up_ATM${ATM}_part0.cvbf.bz2")
 #######################################################
-elif [ ${SIMTYPE} == "CARE_UV_2212" ]; then
+elif [ "${SIMTYPE}" == "CARE_UV_2212" ]; then
     # example gamma_V6_CARE_uvf_Atmosphere61_zen20deg_0.25wob_120MHz.vbf.zst
     LBL="CARE_uvf"
-    VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "gamma_V6_${LBL}_Atmosphere${ATM}_zen${ZA}deg_${WOBBLE}wob_${NOISE}MHz*.zst" -not -name "*.log" -not -name "*.md5sum")
+    VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "gamma_V6_${LBL}_Atmosphere${ATM}_zen${ZA}deg_${WOBBLE}wob_${NOISE}MHz*.zst" -not -name "*.log" -not -name "*.md5sum")
     echo "gamma_V6_${LBL}_Atmosphere${ATM}_zen${ZA}deg_${WOFFSET}wob_${NOISE}MHz"
 #######################################################
-elif [ ${SIMTYPE:0:10} == "CARE_RedHV" ]; then
+elif [ "${SIMTYPE:0:10}" == "CARE_RedHV" ]; then
     # example gamma_V6_PMTUpgrade_RHV_CARE_v1.6.2_12_ATM61_zen40deg_050wob_150MHz.cvbf.zst
     if [[ ${ATM} == 61 ]]; then
         LBL="PMTUpgrade_RHV_CARE_v1.6.2_12"
-        WOFFSET=$(awk -v WB=$WOBBLE 'BEGIN { printf("%03d",100*WB) }')
+        WOFFSET=$(awk -v WB="$WOBBLE" 'BEGIN { printf("%03d",100*WB) }')
     else
         LBL="RHV_CARE_v1.6.2_12"
-        WOFFSET=$(awk -v WB=$WOBBLE 'BEGIN { printf("%02d",10*WB) }')
+        WOFFSET=$(awk -v WB="$WOBBLE" 'BEGIN { printf("%02d",10*WB) }')
     fi
-    VBFNAME=$(find ${SIMDIR}/ -maxdepth 1 -name "gamma_V6_${LBL}_ATM${ATM}_zen${ZA}deg_${WOFFSET}wob_${NOISE}MHz*.zst" -not -name "*.log" -not -name "*.md5sum")
+    VBFNAME=$(find "${SIMDIR}"/ -maxdepth 1 -name "gamma_V6_${LBL}_ATM${ATM}_zen${ZA}deg_${WOFFSET}wob_${NOISE}MHz*.zst" -not -name "*.log" -not -name "*.md5sum")
 #######################################################
-elif [ ${SIMTYPE} == "CARE_June2020" ]; then
-    VBFNAME=$(find ${SIMDIR} -name "*_${WOBBLE}wob_${NOISE}MHz*.zst" -not -name "*.log" -not -name "*.md5sum")
-    echo _${WOFFSET}wob_${NOISE}MHz
-    echo $SIMDIR/Zd${ZA}/merged/Data/
+elif [ "${SIMTYPE}" == "CARE_June2020" ]; then
+    VBFNAME=$(find "${SIMDIR}" -name "*_${WOBBLE}wob_${NOISE}MHz*.zst" -not -name "*.log" -not -name "*.md5sum")
+    echo _"${WOFFSET}"wob_"${NOISE}"MHz
+    echo "$SIMDIR"/Zd"${ZA}"/merged/Data/
 #######################################################
-elif [ ${SIMTYPE:0:4} == "CARE" ]; then
+elif [ "${SIMTYPE:0:4}" == "CARE" ]; then
     # input files (observe that these might need some adjustments)
     if [[ $PARTICLE == "1" ]]; then
-       VBFNAME=$(find ${SIMDIR}/ -name "gamma_${ZA}deg*${WOBBLE}wob_${NOISE}mhz*ATM${ATM}*.zst" -not -name "*.log" -not -name "*.md5sum")
+       VBFNAME=$(find "${SIMDIR}"/ -name "gamma_${ZA}deg*${WOBBLE}wob_${NOISE}mhz*ATM${ATM}*.zst" -not -name "*.log" -not -name "*.md5sum")
     elif [[ $PARTICLE == "2" ]]; then
-       VBFNAME=$(find ${SIMDIR} -name "electron_${ZA}deg*${WOBBLE}wob_${NOISE}mhz*ATM${ATM}*.zst" -not -name "*.log" -not -name "*.md5sum")
+       VBFNAME=$(find "${SIMDIR}" -name "electron_${ZA}deg*${WOBBLE}wob_${NOISE}mhz*ATM${ATM}*.zst" -not -name "*.log" -not -name "*.md5sum")
     elif [[ $PARTICLE == "14" ]]; then
-       VBFNAME=$(find ${SIMDIR} -name "proton_${ZA}deg*${WOBBLE}wob_${NOISE}mhz*ATM${ATM}*.zst" -not -name "*.log" -not -name "*.md5sum")
+       VBFNAME=$(find "${SIMDIR}" -name "proton_${ZA}deg*${WOBBLE}wob_${NOISE}mhz*ATM${ATM}*.zst" -not -name "*.log" -not -name "*.md5sum")
     fi
 fi
 #######################################################
@@ -191,11 +181,11 @@ fi
 for V in ${VBFNAME}
 do
     echo "Processing ${V}"
-    SIMDIR=$(dirname ${V})
+    SIMDIR=$(dirname "${V}")
 
     # size of VBF file
-    FF=$(ls -ls -Llh ${V} | awk '{print $1}' | sed 's/,/./g')
-    V=$(basename ${V})
+    FF=$(du -shL "${V}" | awk '{print $1}' | sed 's/,/./g')
+    V=$(basename "${V}")
     echo "SIMDIR: $SIMDIR"
     echo "VBFILE: ${V} $FF"
     echo "NOISEFILE: ${NOISEFILE}"
@@ -209,7 +199,7 @@ do
        TMSF=$(echo "${FF%?}*25.0" | bc)
     fi
 
-    TMUNI=$(echo "${FF: -1}")
+    TMUNI="${FF: -1}"
     tmpdir_size=${TMSF%.*}$TMUNI
     echo "Setting TMPDIR_SIZE to $tmpdir_size"
 
@@ -220,19 +210,20 @@ do
     FSCRIPT="$LOGDIR/comp-$EPOCH-$SIMTYPE-$ZA-$WOBBLE-$NOISE-ATM$ATM-${RUNNUM}"
     sed -e "s|RUNNUMBER|$RUNNUM|" \
         -e "s|OUTPUTDIR|$OPDIR|" \
-        -e "s|INPUTDIR|$IPDIR|" $SUBSCRIPT.sh > $FSCRIPT.sh
+        -e "s|INPUTDIR|$IPDIR|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
-    chmod u+x $FSCRIPT.sh
-    echo $FSCRIPT.sh
+    chmod u+x "$FSCRIPT".sh
+    echo "$FSCRIPT".sh
 
-    let "RUNNUM = ${RUNNUM} + 100"
+    (( RUNNUM += 100 ))
 
     # run locally or on cluster
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     echo "$SUBC"
     if [[ $SUBC == *qsub* ]]; then
-        JOBID=`$SUBC $FSCRIPT.sh`
+        # shellcheck disable=SC2086
+        JOBID=$($SUBC "$FSCRIPT".sh)
         echo "RUN $RUNNUM: JOBID $JOBID"
     elif [[ $SUBC == *condor* ]]; then
         "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
@@ -243,7 +234,7 @@ do
         echo "-------------------------------------------------------------------------------"
         echo
     elif [[ $SUBC == *parallel* ]]; then
-        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.dat
+        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts.dat
     fi
 done
 echo "LOG/SUBMIT DIR: ${LOGDIR}"
diff --git a/scripts/IRF.dispXGB.sh b/scripts/IRF.dispXGB.sh
index 6fd9f1a..541d2f7 100755
--- a/scripts/IRF.dispXGB.sh
+++ b/scripts/IRF.dispXGB.sh
@@ -2,7 +2,7 @@
 # XGBoost analysis on mscw MC files.
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:59:00; h_vmem=8000M; tmpdir_size=25G
 
 if [ "$#" -lt 3 ]; then
@@ -46,37 +46,36 @@ else
 fi
 
 # make output directory if it doesn't exist
-mkdir -p $ODIR
+mkdir -p "$ODIR"
 echo -e "Output files will be written to:\n $ODIR"
 
 # directory for run scripts
-DATE=`date +"%y%m%d"`
-LOGDIR="$(dirname $INPUTDIR)/submit-XGB-${XGB_TYPE}-${DATE}-$(uuidgen)/"
+DATE=$(date +"%y%m%d")
+LOGDIR="$(dirname "$INPUTDIR")/submit-XGB-${XGB_TYPE}-${DATE}-$(uuidgen)/"
 mkdir -p "$LOGDIR"
 echo -e "Log files will be written to:\n $LOGDIR"
-rm -f ${LOGDIR}/x* 2>/dev/null
+rm -f "${LOGDIR}"/x* 2>/dev/null
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/IRF.dispXGB_sub"
-TIMETAG=`date +"%s"`
 
 for FILE in $FILES
 do
     echo "Now analysing $FILE"
-    FSCRIPT="$LOGDIR/dispXGB-${XGB_TYPE}-$(basename $FILE .root)"
-    rm -f $FSCRIPT.sh
+    FSCRIPT="$LOGDIR/dispXGB-${XGB_TYPE}-$(basename "$FILE" .root)"
+    rm -f "$FSCRIPT".sh
 
     sed -e "s|FFILE|$FILE|" \
         -e "s|XXGB|$XGB|" \
         -e "s|XGB_TTYPE|$XGB_TYPE|" \
         -e "s|ANALYSISTYPE|$ANALYSIS_TYPE|" \
-        -e "s|OODIR|$ODIR|" $SUBSCRIPT.sh > $FSCRIPT.sh
+        -e "s|OODIR|$ODIR|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
     chmod u+x "$FSCRIPT.sh"
-    echo $FSCRIPT.sh
+    echo "$FSCRIPT".sh
 
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     if [[ $SUBC == *condor* ]]; then
         "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
         echo
diff --git a/scripts/IRF.evndisp_MC.sh b/scripts/IRF.evndisp_MC.sh
index 01abdfa..8831ef5 100755
--- a/scripts/IRF.evndisp_MC.sh
+++ b/scripts/IRF.evndisp_MC.sh
@@ -2,7 +2,7 @@
 # submit evndisp for grisu/care simulations
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=47:59:00; h_vmem=8000M; tmpdir_size=50G
 DATE=$(date +"%y%m%d")
 
@@ -54,9 +54,8 @@ fi
 
 # Run init script
 if [ -z "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 
 SIMDIR="$1"
@@ -102,7 +101,7 @@ if [[ ${SIMTYPE:0:5} == "GRISU" ]]; then
     [[ ${EPOCH:0:2} == "V4" ]] && RUNNUM="946500"
     [[ ${EPOCH:0:2} == "V5" ]] && RUNNUM="956500"
     [[ ${EPOCH:0:2} == "V6" ]] && RUNNUM="966500"
-elif [ ${SIMTYPE:0:4} == "CARE" ]; then
+elif [ "${SIMTYPE:0:4}" == "CARE" ]; then
     [[ ${EPOCH:0:2} == "V4" ]] && RUNNUM="941200"
     [[ ${EPOCH:0:2} == "V5" ]] && RUNNUM="951200"
     [[ ${EPOCH:0:2} == "V6" ]] && RUNNUM="961200"
@@ -125,44 +124,44 @@ NOISEFILE="NO_NOISEFILE"
 if [[ ${SIMTYPE:0:5} == "GRISU" ]]; then
     if [[ ${EPOCH:0:2} == "V4" ]] || [[ ${EPOCH:0:2} == "V5" ]]; then
         if [[ ${EPOCH:0:2} == "V5" ]]; then
-            VBFFILENAME="gamma_V5_Oct2012_newArrayConfig_20121027_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*"
+            VBFILENAME="gamma_V5_Oct2012_newArrayConfig_20121027_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*"
         elif [[ $ATM == "21" ]]; then
-            VBFFILENAME="Oct2012_oa_ATM21_${ZA}deg_${INT_WOBBLE}*"
+            VBFILENAME="Oct2012_oa_ATM21_${ZA}deg_${INT_WOBBLE}*"
         else
-            VBFFILENAME="gamma_V4_Oct2012_SummerV4ForProcessing_20130611_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*"
+            VBFILENAME="gamma_V4_Oct2012_SummerV4ForProcessing_20130611_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*"
         fi
         NOISEFILE="$VERITAS_EVNDISP_AUX_DIR/NOISE/NOISE$NOISE.grisu"
     elif [[ ${EPOCH:0:2} == "V6" ]]; then
         if [[ $ATM == "21-redHV" ]]; then
-            VBFFILENAME="gamma_V6_Upgrade_ReducedHV_20121211_v420_ATM21_${ZA}deg_${INT_WOBBLE}*"
+            VBFILENAME="gamma_V6_Upgrade_ReducedHV_20121211_v420_ATM21_${ZA}deg_${INT_WOBBLE}*"
         elif [[ $ATM == "21-UV" ]]; then
-            VBFFILENAME="gamma_V6_Upgrade_UVfilters_20121211_v420_ATM21_${ZA}deg_${INT_WOBBLE}*"
+            VBFILENAME="gamma_V6_Upgrade_UVfilters_20121211_v420_ATM21_${ZA}deg_${INT_WOBBLE}*"
         elif [[ $ATM == "21-SNR" ]]; then
-            VBFFILENAME="gamma_V6_201304_SN2013ak_v420_ATM21_${ZA}deg_${INT_WOBBLE}*"
+            VBFILENAME="gamma_V6_201304_SN2013ak_v420_ATM21_${ZA}deg_${INT_WOBBLE}*"
         else
-            VBFFILENAME="gamma_V6_Upgrade_20121127_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*"
+            VBFILENAME="gamma_V6_Upgrade_20121127_v420_ATM${ATM}_${ZA}deg_${INT_WOBBLE}*"
         fi
         NOISEFILE="$VERITAS_EVNDISP_AUX_DIR/NOISE/NOISE${NOISE}_20120827_v420.grisu"
     fi
 #######################################################
-elif [ ${SIMTYPE} == "CARE_UV_June1409" ]; then
+elif [ "${SIMTYPE}" == "CARE_UV_June1409" ]; then
     # example gamma_00deg_750m_0.5wob_180mhz_up_ATM21_part0.cvbf.bz2
-    WOFFSET=$(awk -v WB=$WOBBLE 'BEGIN { printf("%03d",100*WB) }')
-    VBFFILENAME="gamma_${ZA}deg_750m_${WOFFSET}wob_${NOISE}mhz_up_ATM${ATM}_part0.cvbf.bz2"
-elif [ ${SIMTYPE} == "CARE_UV_2212" ]; then
+    WOFFSET=$(awk -v WB="$WOBBLE" 'BEGIN { printf("%03d",100*WB) }')
+    VBFILENAME="gamma_${ZA}deg_750m_${WOFFSET}wob_${NOISE}mhz_up_ATM${ATM}_part0.cvbf.bz2"
+elif [ "${SIMTYPE}" == "CARE_UV_2212" ]; then
     # example gamma_V6_CARE_uvf_Atmosphere61_zen20deg_0.25wob_120MHz.vbf.zst
     VBFILENAME="gamma_V6_CARE_uvf_Atmosphere${ATM}_zen${ZA}deg_${WOBBLE}wob_${NOISE}MHz*.zst"
-elif [ ${SIMTYPE} == "CARE_RedHV" ]; then
+elif [ "${SIMTYPE}" == "CARE_RedHV" ]; then
     # example gamma_V6_PMTUpgrade_RHV_CARE_v1.6.2_12_ATM61_zen40deg_050wob_150MHz.cvbf.zst
     if [[ ${ATM} == 61 ]]; then
         LBL="PMTUpgrade_RHV_CARE_v1.6.2_12"
-        WOFFSET=$(awk -v WB=$WOBBLE 'BEGIN { printf("%03d",100*WB) }')
+        WOFFSET=$(awk -v WB="$WOBBLE" 'BEGIN { printf("%03d",100*WB) }')
     else
         LBL="RHV_CARE_v1.6.2_12"
-        WOFFSET=$(awk -v WB=$WOBBLE 'BEGIN { printf("%02d",10*WB) }')
+        WOFFSET=$(awk -v WB="$WOBBLE" 'BEGIN { printf("%02d",10*WB) }')
     fi
     VBFILENAME="gamma_V6_${LBL}_ATM${ATM}_zen${ZA}deg_${WOFFSET}wob_${NOISE}MHz*.zst"
-elif [ ${SIMTYPE:0:4} == "CARE" ]; then
+elif [ "${SIMTYPE:0:4}" == "CARE" ]; then
 #    VBFILENAME="*_${WOBBLE}wob_${NOISE}MHz*.zst"
 # Used for processing of pre-2025 simulations (run number starting with 65...)
    VBFILENAME="*_${WOBBLE}wob_${NOISE}MHz_*.vbf.zst"
@@ -171,7 +170,7 @@ elif [ ${SIMTYPE:0:4} == "CARE" ]; then
 #    VBFILENAME="*_${WOBBLE}wob_${NOISE}MHz_66*.zst"
 fi
 echo "VBF file name search string: $VBFILENAME"
-VBFNAME=$(find ${SIMDIR} -name "$VBFILENAME" -not -name "*.log" -not -name "*.md5sum")
+VBFNAME=$(find "${SIMDIR}" -name "$VBFILENAME" -not -name "*.log" -not -name "*.md5sum")
 if [[ -z "$VBFNAME" ]]; then
     echo "No vbf files found"
     exit
@@ -194,8 +193,8 @@ rm -f "${FSCRIPT}.txt"
 touch "${FSCRIPT}.txt"
 
 for V in $VBFNAME; do
-    echo "$RUNNUM $(basename $V)" >> "${FSCRIPT}.txt"
-    let "RUNNUM = ${RUNNUM} + 100"
+    echo "$RUNNUM $(basename "$V")" >> "${FSCRIPT}.txt"
+    (( RUNNUM += 100 ))
 done
 
 # Job submission script
@@ -212,7 +211,7 @@ sed -e "s|DATADIR|$SIMDIR|" \
     -e "s|SIMULATIONTYPE|$SIMTYPE|" \
     -e "s|VVERSION|$EDVERSION|" \
     -e "s|ADDITIONALOPTIONS|$EDOPTIONS|" \
-    -e "s|NOISEFFILE|$NOISEFILE|"  $SUBSCRIPT > $FSCRIPT
+    -e "s|NOISEFFILE|$NOISEFILE|"  "$SUBSCRIPT" > "$FSCRIPT"
 
 chmod u+x "$FSCRIPT"
 echo "Run script: $FSCRIPT"
@@ -223,7 +222,7 @@ if [[ $SUBC == *"condor"* ]]; then
     SUBFIL=${SUBSCRIPT}.condor
     [[ -f "$SUBFIL" ]] && rm -f "$SUBFIL"
 
-cat > ${SUBFIL} <<EOL
+cat > "${SUBFIL}" <<EOL
 Executable = ${SUBSCRIPT}
 Output = ${SUBSCRIPT}.\$(Cluster)_\$(Process).output
 Error = ${SUBSCRIPT}.\$(Cluster)_\$(Process).error
diff --git a/scripts/IRF.generalproduction.sh b/scripts/IRF.generalproduction.sh
index acf7128..7d49ed6 100755
--- a/scripts/IRF.generalproduction.sh
+++ b/scripts/IRF.generalproduction.sh
@@ -38,7 +38,7 @@ IRFTYPE=$2
 
 process_irfs()
 {
-    EPOCHS=$(cat $4 | sort -u)
+    EPOCHS=$(cat "$4" | sort -u)
     # FIX EPOCHS="V6_2023_2023s"
     for E in $EPOCHS
     do
@@ -50,36 +50,36 @@ process_irfs()
                 continue
             fi
         fi
-        echo $E $1 $2 $3
+        echo "$E" "$1" "$2" "$3"
         if [[ "$1" == "ANALYSETABLES" ]] || [[ "$1" == "EFFECTIVEAREAS" ]] || [[ "$1" == "COMBINEEFFECTIVEAREAS" ]]; then
             for ID in 0 2 3 4 5
             do
-                ./IRF.production.sh $2 $1 $E $3 $ID
+                ./IRF.production.sh "$2" "$1" "$E" "$3" $ID
             done
         else
-            ./IRF.production.sh $2 $1 $E $3 0
+            ./IRF.production.sh "$2" "$1" "$E" "$3" 0
         fi
     done
 }
 
 if [[ ${SIMTYPE} == "CARE_UV_2212" ]]; then
-    process_irfs ${IRFTYPE} ${SIMTYPE} 61 $VERITAS_EVNDISP_AUX_DIR/IRF_EPOCHS_obsfilter.dat
+    process_irfs "${IRFTYPE}" "${SIMTYPE}" 61 "$VERITAS_EVNDISP_AUX_DIR"/IRF_EPOCHS_obsfilter.dat
 elif [[ ${SIMTYPE} == "GRISU" ]]; then
     if [[ "$2" == "ANALYSETABLES" ]] || [[ "$2" == "EFFECTIVEAREAS" ]] || [[ "$2" == "COMBINEEFFECTIVEAREAS" ]]; then
         for ID in 0 2 3 4 5
         do
-            ./IRF.production.sh GRISU ${IRFTYPE} V5 21 $ID
-            ./IRF.production.sh GRISU ${IRFTYPE} V5 22 $ID
-            ./IRF.production.sh GRISU ${IRFTYPE} V4 21 $ID
-            ./IRF.production.sh GRISU ${IRFTYPE} V4 22 $ID
+            ./IRF.production.sh GRISU "${IRFTYPE}" V5 21 $ID
+            ./IRF.production.sh GRISU "${IRFTYPE}" V5 22 $ID
+            ./IRF.production.sh GRISU "${IRFTYPE}" V4 21 $ID
+            ./IRF.production.sh GRISU "${IRFTYPE}" V4 22 $ID
         done
     else
-            ./IRF.production.sh GRISU ${IRFTYPE} V5 21 0
-            ./IRF.production.sh GRISU ${IRFTYPE} V5 22 0
-            ./IRF.production.sh GRISU ${IRFTYPE} V4 21 0
-            ./IRF.production.sh GRISU ${IRFTYPE} V4 22 0
+            ./IRF.production.sh GRISU "${IRFTYPE}" V5 21 0
+            ./IRF.production.sh GRISU "${IRFTYPE}" V5 22 0
+            ./IRF.production.sh GRISU "${IRFTYPE}" V4 21 0
+            ./IRF.production.sh GRISU "${IRFTYPE}" V4 22 0
     fi
 else
-    process_irfs ${IRFTYPE} ${SIMTYPE} 61 $VERITAS_EVNDISP_AUX_DIR/IRF_EPOCHS_WINTER.dat
-    process_irfs ${IRFTYPE} ${SIMTYPE} 62 $VERITAS_EVNDISP_AUX_DIR/IRF_EPOCHS_SUMMER.dat
+    process_irfs "${IRFTYPE}" "${SIMTYPE}" 61 "$VERITAS_EVNDISP_AUX_DIR"/IRF_EPOCHS_WINTER.dat
+    process_irfs "${IRFTYPE}" "${SIMTYPE}" 62 "$VERITAS_EVNDISP_AUX_DIR"/IRF_EPOCHS_SUMMER.dat
 fi
diff --git a/scripts/IRF.generate_NOISEfiles_from_PedestalEvents.sh b/scripts/IRF.generate_NOISEfiles_from_PedestalEvents.sh
index 2d50487..7868c2c 100755
--- a/scripts/IRF.generate_NOISEfiles_from_PedestalEvents.sh
+++ b/scripts/IRF.generate_NOISEfiles_from_PedestalEvents.sh
@@ -15,7 +15,7 @@
 # - length of noise traces
 ##############################################################
 # EventDisplay version
-EDVERSION=`$EVNDISPSYS/bin/evndisp --version | tr -d .`
+EDVERSION=$("$EVNDISPSYS"/bin/evndisp --version | tr -d .)
 if [[ $EDVERSION = "v4"* ]]; then
    echo "Noise file writer not implemented for Eventdisplay version $EDVERSION"
    exit
@@ -53,6 +53,6 @@ do
     echo "reading $IFIL"
     echo "writing $OFIL"
 
-    $EVNDISPSYS/bin/VTS.NoiseFileWriter 4 499 $IFIL $OFIL $TLENGTH
+    "$EVNDISPSYS"/bin/VTS.NoiseFileWriter 4 499 "$IFIL" "$OFIL" $TLENGTH
 
 done
diff --git a/scripts/IRF.generate_effective_area_parts.sh b/scripts/IRF.generate_effective_area_parts.sh
index 34c0134..904a901 100755
--- a/scripts/IRF.generate_effective_area_parts.sh
+++ b/scripts/IRF.generate_effective_area_parts.sh
@@ -3,11 +3,11 @@
 # (output need to be combined afterwards)
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=13:29:00; h_vmem=8000M; tmpdir_size=20G
 
 # EventDisplay version
-IRFVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+IRFVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 if [ $# -lt 8 ]; then
 echo "
@@ -53,9 +53,8 @@ fi
 
 # Run init script
 if [ -z "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 CUTSFILE="$1"
 EPOCH="$2"
@@ -96,7 +95,7 @@ MCFILE="${INDIR}/${ZA}deg_${WOBBLE}wob_NOISE${NOISE}.mscw.root"
 # effective area output file
 EFFAREAFILE="EffArea-${SIMTYPE}-${EPOCH}-ID${RECID}-Ze${ZA}deg-${WOBBLE}wob-${NOISE}"
 # name of cut
-CUTS_NAME=$(basename $CUTSFILE)
+CUTS_NAME=$(basename "$CUTSFILE")
 CUTS_NAME=${CUTS_NAME##ANASUM.GammaHadron-}
 CUTS_NAME=${CUTS_NAME%%.dat}
 echo "Cuts: $CUTSFILE $CUTS_NAME"
@@ -113,7 +112,7 @@ sed -e "s|OUTPUTDIR|$ODIR|" \
     -e "s|STEREOXGB|$XGBSTEREOFILESUFFIX|" \
     -e "s|GHXGB|$XGBGAMMAHADRONFILESUFFIX|" \
     -e "s|DATAFILE|$MCFILE|" \
-    -e "s|GAMMACUTS|${CUTSFILE}|" $SUBSCRIPT.sh > $FSCRIPT
+    -e "s|GAMMACUTS|${CUTSFILE}|" "$SUBSCRIPT".sh > "$FSCRIPT"
 
 chmod u+x "$FSCRIPT"
 echo "Run script: $FSCRIPT"
@@ -126,7 +125,8 @@ if [[ $SUBC == *"ERROR"* ]]; then
     exit 1
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT")
     echo "JOBID: $JOBID"
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT" "$h_vmem" "$tmpdir_size"
@@ -135,9 +135,10 @@ elif [[ $SUBC == *condor* ]]; then
     echo "$EVNDISPSCRIPTS/helper_scripts/submit_scripts_to_htcondor.sh ${LOGDIR} submit"
     echo "-------------------------------------------------------------------------------"
 elif [[ $SUBC == *sbatch* ]]; then
-    $SUBC $FSCRIPT
+    # shellcheck disable=SC2086
+    $SUBC "$FSCRIPT"
 elif [[ $SUBC == *parallel* ]]; then
-    echo "$FSCRIPT &> $(basename $FSCRIPT .sh).log" >> "$LOGDIR/runscripts.dat"
+    echo "$FSCRIPT &> $(basename "$FSCRIPT" .sh).log" >> "$LOGDIR/runscripts.dat"
 elif [[ "$SUBC" == *simple* ]]; then
-    "$FSCRIPT" | tee "$(basename $FSCRIPT .sh).log"
+    "$FSCRIPT" | tee "$(basename "$FSCRIPT" .sh).log"
 fi
diff --git a/scripts/IRF.generate_lookup_table_parts.sh b/scripts/IRF.generate_lookup_table_parts.sh
index 798b92c..4c08c9a 100755
--- a/scripts/IRF.generate_lookup_table_parts.sh
+++ b/scripts/IRF.generate_lookup_table_parts.sh
@@ -3,11 +3,11 @@
 # (generated tables need to be combined afterwards)
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=03:29:00; h_vmem=12000M; tmpdir_size=20G
 
 # EventDisplay version
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 EVNIRFVERSION="v4N"
 
 if [ $# -lt 7 ]; then
@@ -47,9 +47,8 @@ fi
 
 # Run init script
 if [ -z "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 EPOCH="$1"
 ATM="$2"
@@ -113,7 +112,8 @@ if [[ $SUBC == *"ERROR"* ]]; then
     exit 1
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT")
     echo "JOBID: $JOBID"
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT" "$h_vmem" "$tmpdir_size"
@@ -122,7 +122,8 @@ elif [[ $SUBC == *condor* ]]; then
     echo "$EVNDISPSCRIPTS/helper_scripts/submit_scripts_to_htcondor.sh ${LOGDIR} submit"
     echo "-------------------------------------------------------------------------------"
 elif [[ $SUBC == *sbatch* ]]; then
-    $SUBC $FSCRIPT
+    # shellcheck disable=SC2086
+    $SUBC "$FSCRIPT"
 elif [[ $SUBC == *parallel* ]]; then
     echo "$FSCRIPT &> $FSCRIPT.log" >> "$LOGDIR/runscripts.dat"
 elif [[ "$SUBC" == *simple* ]]; then
diff --git a/scripts/IRF.generate_radial_acceptance.sh b/scripts/IRF.generate_radial_acceptance.sh
index 0a8f087..9053982 100755
--- a/scripts/IRF.generate_radial_acceptance.sh
+++ b/scripts/IRF.generate_radial_acceptance.sh
@@ -2,7 +2,7 @@
 # calculate radial acceptances
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=04:29:00; h_vmem=6000M; tmpdir_size=10G
 
 if [[ $# != 6 ]]; then
@@ -49,8 +49,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 RLIST=$1
@@ -60,7 +59,7 @@ EPOCH=$4
 SIM=$5
 RECID="$6"
 # make radial acceptance version
-IRFVERSION=`$EVNDISPSYS/bin/makeRadialAcceptance --version | tr -d . | sed -e 's/[a-Z]*$//'`
+IRFVERSION=$("$EVNDISPSYS"/bin/makeRadialAcceptance --version | tr -d . | sed -e 's/[a-Z]*$//')
 # version string for aux files
 AUX="auxv01"
 
@@ -81,7 +80,7 @@ fi
 CUTLIST=$(IFS=$'\r\n'; cat "$CUTLISTFILE")
 
 # run scripts and logs are written into this directory
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/$DATE/RADIAL"
 echo -e "Log files will be written to:\n $LOGDIR"
 mkdir -p "$LOGDIR"
@@ -110,7 +109,7 @@ for CUTS in "${CUTLIST[@]}"; do
 
             # Check that cuts file exists
             CUTSFILE=${CUTS%%.dat}.dat
-            if [[ "$CUTSFILE" == `basename $CUTSFILE` ]]; then
+            if [[ "$CUTSFILE" == $(basename "$CUTSFILE") ]]; then
                 CUTSFILE="$VERITAS_EVNDISP_AUX_DIR/GammaHadronCutFiles/$CUTSFILE"
             fi
             if [[ ! -f "$CUTSFILE" ]]; then
@@ -120,16 +119,16 @@ for CUTS in "${CUTLIST[@]}"; do
             fi
 
             METH="${VERITAS_ANALYSIS_TYPE/_/-}"
-	        CUTSNAME=`basename $CUTSFILE`
+	        CUTSNAME=$(basename "$CUTSFILE")
             # Generate base file name based on cuts file, extended and point source radial acceptances are the same
             CUTSNAME=${CUTSNAME##ANASUM.GammaHadron-}
             CUTSNAME=${CUTSNAME%%.dat}
             if [[ $CUTSNAME == *PointSource-* ]] ; then
                 CUTSNAME=${CUTSNAME/-PointSource-/"-"}
-                echo $CUTSNAME
+                echo "$CUTSNAME"
             elif [[ $CUTSNAME == *ExtendedSource-* ]]; then
                 CUTSNAME=${CUTSNAME/-ExtendedSource-/"-"}
-                echo $CUTSNAME
+                echo "$CUTSNAME"
             fi
             OFILE="radialAcceptance-${IRFVERSION}-${AUX}-${SIM}-$CUTSNAME-${METH}-$VX-T$TELES"
             ODIR="$VERITAS_IRFPRODUCTION_DIR/${IRFVERSION}/${VERITAS_ANALYSIS_TYPE:0:2}/RadialAcceptances"
@@ -144,30 +143,32 @@ for CUTS in "${CUTLIST[@]}"; do
                 -e "s|CUTSFILE|$CUTSFILE|" \
                 -e "s|OUTPUTDIR|$ODIR|"    \
 		        -e "s|TELTOANA|$TELES|" \
-                -e "s|OUTPUTFILE|$OFILE|" $SUBSCRIPT > $FSCRIPT.sh
+                -e "s|OUTPUTFILE|$OFILE|" "$SUBSCRIPT" > "$FSCRIPT".sh
 
-            chmod u+x $FSCRIPT.sh
+            chmod u+x "$FSCRIPT".sh
             echo "Script submitted to cluster: $FSCRIPT.sh"
 
             # run locally or on cluster
             SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
             echo "$LOGDIR"
-            SUBC=`eval "echo \"$SUBC\""`
+            SUBC=$(eval "echo \"$SUBC\"")
             if [[ $SUBC == *"ERROR"* ]]; then
-                echo $SUBC
+                echo "$SUBC"
                 exit
             fi
             if [[ $SUBC == *qsub* ]]; then
                 echo "$SUBC" "$FSCRIPT.sh"
-                JOBID=`$SUBC $FSCRIPT.sh`
+                # shellcheck disable=SC2086
+                JOBID=$($SUBC "$FSCRIPT".sh)
                 echo "JOBID: $JOBID"
             elif [[ $SUBC == *condor* ]]; then
                 "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-                condor_submit $FSCRIPT.sh.condor
-	        elif [[ $SUBC == *sbatch* ]]; then
-	         	$SUBC $FSCRIPT.sh
+                condor_submit "$FSCRIPT".sh.condor
+            elif [[ $SUBC == *sbatch* ]]; then
+                # shellcheck disable=SC2086
+                $SUBC "$FSCRIPT".sh
             elif [[ $SUBC == *parallel* ]]; then
-                echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.dat
+                echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts.dat
             fi
         done
     done
@@ -175,7 +176,8 @@ done
 
 # Execute all FSCRIPTs locally in parallel
 if [[ $SUBC == *parallel* ]]; then
-    cat "$LOGDIR/runscripts.dat" | "$SUBC"
+    # shellcheck disable=SC2086
+    cat "$LOGDIR/runscripts.dat" | $SUBC
 fi
 
 exit
diff --git a/scripts/IRF.mscw_energy_MC.sh b/scripts/IRF.mscw_energy_MC.sh
index c0d1acd..3683b8f 100755
--- a/scripts/IRF.mscw_energy_MC.sh
+++ b/scripts/IRF.mscw_energy_MC.sh
@@ -3,11 +3,11 @@
 # Allow optionally to calculate instrument response functions (for 4 and 3-telescope combinations).
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=10:29:00; h_vmem=12000M; tmpdir_size=100G
 
 # EventDisplay version
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 EVNIRFVERSION="v4N"
 
 if [ $# -lt 8 ]; then
@@ -55,9 +55,8 @@ fi
 
 # Run init script
 if [ -z "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 TABFILE=${1%.root}.root
 EPOCH="$2"
@@ -75,7 +74,7 @@ XGBVERSION="xgb"
 
 echo "IRF.mscw_energy_MC for epoch $EPOCH, atmo $ATM, zenith $ZA, wobble $WOBBLE, noise $NOISE (DISP: $DISPBDT, XGB $XGBVERSION)"
 
-TABFILE="$VERITAS_EVNDISP_AUX_DIR/Tables/$(basename $TABFILE)"
+TABFILE="$VERITAS_EVNDISP_AUX_DIR/Tables/$(basename "$TABFILE")"
 if [[ ! -f "$TABFILE" ]]; then
     echo "Error: table file not found: $TABFILE"
     exit 1
@@ -138,7 +137,8 @@ if [[ $SUBC == *"ERROR"* ]]; then
     exit 1
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT")
     echo "JOBID: $JOBID"
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT" "$h_vmem" "$tmpdir_size"
@@ -147,7 +147,8 @@ elif [[ $SUBC == *condor* ]]; then
     echo "$EVNDISPSCRIPTS/helper_scripts/submit_scripts_to_htcondor.sh ${LOGDIR} submit"
     echo "-------------------------------------------------------------------------------"
 elif [[ $SUBC == *sbatch* ]]; then
-    $SUBC $FSCRIPT
+    # shellcheck disable=SC2086
+    $SUBC "$FSCRIPT"
 elif [[ $SUBC == *parallel* ]]; then
     echo "$FSCRIPT &> $FSCRIPT.log" >> "$LOGDIR/runscripts.dat"
 elif [[ "$SUBC" == *simple* ]]; then
diff --git a/scripts/IRF.optimizeTMVAforGammaHadronSeparation.sh b/scripts/IRF.optimizeTMVAforGammaHadronSeparation.sh
index 0724b37..fe92642 100755
--- a/scripts/IRF.optimizeTMVAforGammaHadronSeparation.sh
+++ b/scripts/IRF.optimizeTMVAforGammaHadronSeparation.sh
@@ -3,7 +3,7 @@
 #
 #
 
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:59:59; h_vmem=4000M; tmpdir_size=1G
 
 if [[ $# -lt 5 ]]; then
@@ -32,8 +32,7 @@ exit
 fi
 echo " "
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 PREDIR=$1
@@ -42,16 +41,7 @@ SIMTYPE=$3
 EPOCH=$4
 ATM=$5
 # evndisplay version
-IRFVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
-
-DISPBDT=""
-ANATYPE="AP"
-if [[ ! -z $VERITAS_ANALYSIS_TYPE ]]; then
-    ANATYPE="${VERITAS_ANALYSIS_TYPE:0:2}"
-    if [[ ${VERITAS_ANALYSIS_TYPE} == *"DISP"* ]]; then
-        DISPBDT="_DISP"
-    fi
-fi
+IRFVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 # Check that list of background files exists
 if [[ ! -d "${PREDIR}/${CUTTYPE}" ]]; then
@@ -61,10 +51,10 @@ fi
 
 #####################################
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$PREDIR/${CUTTYPE}/$DATE/"
 echo -e "Log files will be written to:\n $LOGDIR"
-mkdir -p $LOGDIR
+mkdir -p "$LOGDIR"
 
 # EffAreaFile
 if [[ $CUTTYPE == *"Moderate"* ]]; then
@@ -90,36 +80,22 @@ else
 fi
 #####################################
 # energy bins
+count1=1
 if grep -q "^\* ENERGYBINS" "$RUNPAR"; then
     ENBINS=$( cat "$RUNPAR" | grep "^\* ENERGYBINS" | sed -e 's/\* ENERGYBINS//' | sed -e 's/ /\n/g')
     mapfile -t EBINARRAY <<< "$ENBINS"
-    count1=1
-    NENE=$((${#EBINARRAY[@]}-$count1)) #get number of bins
-    for (( i=0; i < $NENE; i++ ))
-    do
-        EBINMIN[$i]=${EBINARRAY[$i]}
-        EBINMAX[$i]=${EBINARRAY[$i+1]}
-    done
+    NENE=$(( ${#EBINARRAY[@]}-count1 )) #get number of bins
 else
     ENBINS=$( cat "$RUNPAR" | grep "^* ENERGYBINEDGES" | sed -e 's/* ENERGYBINEDGES//' | sed -e 's/ /\n/g')
     mapfile -t EBINARRAY <<< "$ENBINS"
-    count1=1
-    NENE=$((${#EBINARRAY[@]}-$count1)) #get number of bins
-    z="0"
-    for (( i=0; i < $NENE; i+=2 ))
-    do
-        EBINMIN[$z]=${EBINARRAY[$i]}
-        EBINMAX[$z]=${EBINARRAY[$i+1]}
-        let "z = ${z} + 1"
-    done
-    NENE=$((${#EBINMAX[@]}))
+    NENE=$(( ${#EBINARRAY[@]} / 2 ))
 fi
 
 #####################################
 # zenith angle bins
 ZEBINS=$( cat "$RUNPAR" | grep "^* ZENBINS " | sed -e 's/* ZENBINS//' | sed -e 's/ /\n/g')
 mapfile -t ZEBINARRAY <<< "$ZEBINS"
-NZEW=$((${#ZEBINARRAY[@]}-$count1)) #get number of bins
+NZEW=$(( ${#ZEBINARRAY[@]}-count1 )) #get number of bins
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/IRF.optimizeTMVAforGammaHadronSeparation_sub"
@@ -132,20 +108,21 @@ sed -e "s|EFFFILE|$EFFFILE|"  \
     -e "s|EEBINS|${NENE}|" \
     -e "s|ZZBINS|${NZEW}|" \
     -e "s|TMVARUNPARA|${RUNPAR}|" \
-    -e "s|CUTTYPE|${CUTTYPE}|" $SUBSCRIPT.sh > $FSCRIPT.sh
+    -e "s|CUTTYPE|${CUTTYPE}|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
-chmod u+x $FSCRIPT.sh
-echo $FSCRIPT.sh
+chmod u+x "$FSCRIPT".sh
+echo "$FSCRIPT".sh
 
 # run locally or on cluster
 SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-SUBC=`eval "echo \"$SUBC\""`
+SUBC=$(eval "echo \"$SUBC\"")
 if [[ $SUBC == *"ERROR"* ]]; then
-    echo $SUBC
+    echo "$SUBC"
     exit
 fi
 if [[ $SUBC == *qsub* ]]; then
- JOBID=`$SUBC $FSCRIPT.sh`
+ # shellcheck disable=SC2086
+ JOBID=$($SUBC "$FSCRIPT".sh)
  # account for -terse changing the job number format
  if [[ $SUBC != *-terse* ]] ; then
     echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
@@ -154,12 +131,14 @@ if [[ $SUBC == *qsub* ]]; then
  echo "JOBID:  $JOBID"
 elif [[ $SUBC == *condor* ]]; then
    "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-   condor_submit $FSCRIPT.sh.condor
+   condor_submit "$FSCRIPT".sh.condor
 elif [[ $SUBC == *sbatch* ]]; then
-    $SUBC $FSCRIPT.sh
+    # shellcheck disable=SC2086
+    $SUBC "$FSCRIPT".sh
 elif [[ $SUBC == *parallel* ]]; then
-    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.dat
-    cat $LOGDIR/runscripts.dat | $SUBC
+    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts.dat
+    # shellcheck disable=SC2086
+    cat "$LOGDIR"/runscripts.dat | $SUBC
 elif [[ "$SUBC" == *simple* ]] ; then
     "$FSCRIPT.sh" | tee "$FSCRIPT.log"
 fi
diff --git a/scripts/IRF.production.sh b/scripts/IRF.production.sh
index e72548e..a11adc3 100755
--- a/scripts/IRF.production.sh
+++ b/scripts/IRF.production.sh
@@ -3,7 +3,7 @@
 # IRF production script (VERITAS)
 
 # EventDisplay version
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 if [ $# -lt 2 ]; then
 echo "
@@ -70,9 +70,8 @@ cd "$(dirname "$0")" || exit
 
 # Run init script
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
-    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
+    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 # Parse command line arguments
 SIMTYPE="$1"
@@ -84,7 +83,7 @@ IRFTYPE="$2"
 [[ "$7" ]] && SIMDIR="$7" || SIMDIR=""
 
 # uuid for this job batch
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 UUID=${DATE}-$(uuidgen)
 
 # version string for aux files
@@ -149,25 +148,25 @@ elif [ "${SIMTYPE}" = "CARE_June1702" ]; then
     WOBBLE_OFFSETS=( 0.5 )
 elif [ "${SIMTYPE}" == "CARE_UV_June1409" ]; then
     SIMDIR=${VERITAS_DATA_DIR}/simulations/V6_FLWO/CARE_June1409_UV/
-    ZENITH_ANGLES=$(ls ${SIMDIR}/*.bz2 | awk -F "gamma_" '{print $2}' | awk -F "deg." '{print $1}' | sort | uniq)
-    NSB_LEVELS=$(ls ${SIMDIR}/*.bz2 | awk -F "wob_" '{print $2}' | awk -F "mhz." '{print $1}' | sort | uniq)
+    ZENITH_ANGLES=$(find "${SIMDIR}" -maxdepth 1 -name "*.bz2" -exec basename {} \; | awk -F "gamma_" '{print $2}' | awk -F "deg." '{print $1}' | sort | uniq)
+    NSB_LEVELS=$(find "${SIMDIR}" -maxdepth 1 -name "*.bz2" -exec basename {} \; | awk -F "wob_" '{print $2}' | awk -F "mhz." '{print $1}' | sort | uniq)
     WOBBLE_OFFSETS=( 0.5 )
 elif [ "${SIMTYPE}" == "CARE_UV_2212" ]; then
     SIMDIR=${VERITAS_DATA_DIR}/simulations/UVF_Dec2022/CARE/
-    ZENITH_ANGLES=$(ls ${SIMDIR}/*.zst | awk -F "_zen" '{print $2}' | awk -F "deg." '{print $1}' | sort | uniq)
-    NSB_LEVELS=$(ls ${SIMDIR}/*.zst | awk -F "wob_" '{print $2}' | awk -F "MHz." '{print $1}' | sort | uniq)
-    WOBBLE_OFFSETS=$(ls ${SIMDIR}/*.zst | awk -F "_" '{print $8}' |  awk -F "wob" '{print $1}' | sort -u)
+    ZENITH_ANGLES=$(find "${SIMDIR}" -maxdepth 1 -name "*.zst" -exec basename {} \; | awk -F "_zen" '{print $2}' | awk -F "deg." '{print $1}' | sort | uniq)
+    NSB_LEVELS=$(find "${SIMDIR}" -maxdepth 1 -name "*.zst" -exec basename {} \; | awk -F "wob_" '{print $2}' | awk -F "MHz." '{print $1}' | sort | uniq)
+    WOBBLE_OFFSETS=$(find "${SIMDIR}" -maxdepth 1 -name "*.zst" -exec basename {} \; | awk -F "_" '{print $8}' | awk -F "wob" '{print $1}' | sort -u)
 elif [ "${SIMTYPE}" == "CARE_RedHV" ]; then
     SIMDIR="${VERITAS_DCACHE_DIR}/simulations/V6_FLWO/CARE_June1702_RHV/ATM${ATMOS}"
-    ZENITH_ANGLES=$(ls ${SIMDIR}/*.zst | awk -F "_zen" '{print $2}' | awk -F "deg." '{print $1}' | sort | uniq)
-    NSB_LEVELS=$(ls ${SIMDIR}/*.zst | awk -F "wob_" '{print $2}' | awk -F "MHz." '{print $1}' | sort | uniq)
+    ZENITH_ANGLES=$(find "${SIMDIR}" -maxdepth 1 -name "*.zst" -exec basename {} \; | awk -F "_zen" '{print $2}' | awk -F "deg." '{print $1}' | sort | uniq)
+    NSB_LEVELS=$(find "${SIMDIR}" -maxdepth 1 -name "*.zst" -exec basename {} \; | awk -F "wob_" '{print $2}' | awk -F "MHz." '{print $1}' | sort | uniq)
     WOBBLE_OFFSETS=( 0.5 )
 elif [[ "${SIMTYPE}" == "CARE_June2020" ]]; then
     SIMDIR="${VERITAS_DATA_DIR}/shared/simulations/NSOffsetSimulations/Atmosphere${ATMOS}"
-    ZENITH_ANGLES=$(ls ${SIMDIR} | awk -F "Zd" '{print $2}' | sort | uniq)
-    set -- $ZENITH_ANGLES
-    NSB_LEVELS=$(ls ${SIMDIR}/Zd*/* | awk -F "_" '{print $8}' | awk -F "MHz" '{print $1}'| sort -u)
-    WOBBLE_OFFSETS=$(ls ${SIMDIR}/Zd*/* | awk -F "_" '{print $7}' |  awk -F "wob" '{print $1}' | sort -u)
+    ZENITH_ANGLES=$(find "${SIMDIR}" -mindepth 1 -maxdepth 1 -type d -name "Zd*" -exec basename {} \; | awk -F "Zd" '{print $2}' | sort | uniq)
+    set -- "$ZENITH_ANGLES"
+    NSB_LEVELS=$(find "${SIMDIR}" -path '*/Zd*/*' -type f -exec basename {} \; | awk -F "_" '{print $8}' | awk -F "MHz" '{print $1}' | sort -u)
+    WOBBLE_OFFSETS=$(find "${SIMDIR}" -path '*/Zd*/*' -type f -exec basename {} \; | awk -F "_" '{print $7}' | awk -F "wob" '{print $1}' | sort -u)
     ######################################
     # TEST
     # ZENITH_ANGLES=( 20 )
@@ -188,13 +187,13 @@ elif [[ "${SIMTYPE}" == "CARE_June2020" ]]; then
     ######################################
 elif [[ "${SIMTYPE}" == "CARE_RedHV_Feb2024" ]]; then
     SIMDIR="${VERITAS_DCACHE_DIR}/simulations/NSOffsetSimulations_redHV/Atmosphere${ATMOS}"
-    ZENITH_ANGLES=$(ls ${SIMDIR} | awk -F "Zd" '{print $2}' | grep -v curved | sort | uniq)
+    ZENITH_ANGLES=$(find "${SIMDIR}" -mindepth 1 -maxdepth 1 -type d -name "Zd*" -exec basename {} \; | awk -F "Zd" '{print $2}' | grep -v curved | sort | uniq)
     # ZENITH_ANGLES=( 60 65 )
-    set -- $ZENITH_ANGLES
-    ze_first_bin=$(echo $ZENITH_ANGLES | awk '{print $1}')
+    set -- "$ZENITH_ANGLES"
+    ze_first_bin=$(echo "$ZENITH_ANGLES" | awk '{print $1}')
     # Note! Assumes same NSB and WOBBLE offsets for flat and curved atmosphere
-    NSB_LEVELS=$(ls ${SIMDIR}/Zd${ze_first_bin}/*vbf.zst | awk -F "_" '{print $9}' | awk -F "MHz" '{print $1}'| sort -u)
-    WOBBLE_OFFSETS=$(ls ${SIMDIR}/Zd${ze_first_bin}/*.vbf.zst | awk -F "_" '{print $8}' |  awk -F "wob" '{print $1}' | sort -u)
+    NSB_LEVELS=$(find "${SIMDIR}/Zd${ze_first_bin}" -maxdepth 1 -name "*vbf.zst" -exec basename {} \; | awk -F "_" '{print $9}' | awk -F "MHz" '{print $1}' | sort -u)
+    WOBBLE_OFFSETS=$(find "${SIMDIR}/Zd${ze_first_bin}" -maxdepth 1 -name "*.vbf.zst" -exec basename {} \; | awk -F "_" '{print $8}' | awk -F "wob" '{print $1}' | sort -u)
     ######################################
     # TEST
     # NSB_LEVELS=( 300 )
@@ -202,12 +201,12 @@ elif [[ "${SIMTYPE}" == "CARE_RedHV_Feb2024" ]]; then
     # WOBBLE_OFFSETS=( 0.5 )
 elif [[ "${SIMTYPE}" == "CARE_202404" ]] || [[ "${SIMTYPE}" == "CARE_24_20" ]]; then
     SIMDIR="${VERITAS_DCACHE_DIR}/simulations/NSOffsetSimulations_202404/Atmosphere${ATMOS}"
-    ZENITH_ANGLES=$(ls ${SIMDIR} | awk -F "Zd" '{print $2}' | grep -v curved | sort | uniq)
-    set -- $ZENITH_ANGLES
-    ze_first_bin=$(echo $ZENITH_ANGLES | awk '{print $1}')
+    ZENITH_ANGLES=$(find "${SIMDIR}" -mindepth 1 -maxdepth 1 -type d -name "Zd*" -exec basename {} \; | awk -F "Zd" '{print $2}' | grep -v curved | sort | uniq)
+    set -- "$ZENITH_ANGLES"
+    ze_first_bin=$(echo "$ZENITH_ANGLES" | awk '{print $1}')
     # assume same NSB and wobble offsets in all bins
-    NSB_LEVELS=$(ls ${SIMDIR}/*${ze_first_bin}*/* | awk -F "_" '{print $9}' | awk -F "MHz" '{print $1}'| sort -u)
-    WOBBLE_OFFSETS=$(ls ${SIMDIR}/*${ze_first_bin}*/* | awk -F "_" '{print $8}' |  awk -F "wob" '{print $1}' | sort -u)
+    NSB_LEVELS=$(find "${SIMDIR}" -path "*${ze_first_bin}*/*" -type f -exec basename {} \; | awk -F "_" '{print $9}' | awk -F "MHz" '{print $1}' | sort -u)
+    WOBBLE_OFFSETS=$(find "${SIMDIR}" -path "*${ze_first_bin}*/*" -type f -exec basename {} \; | awk -F "_" '{print $8}' | awk -F "wob" '{print $1}' | sort -u)
     ######################################
     # TEST
     # ZENITH_ANGLES=( 00 20 30 35 40 45 )
@@ -220,7 +219,7 @@ elif [[ "${SIMTYPE}" == "CARE_202404" ]] || [[ "${SIMTYPE}" == "CARE_24_20" ]];
     # NSB_LEVELS=( 200 )
     ######################################
     # TRAINMVANGRES production
-elif [ ${SIMTYPE:0:4} == "CARE" ]; then
+elif [ "${SIMTYPE:0:4}" == "CARE" ]; then
     # Older CARE simulation parameters
     SIMDIR=$VERITAS_DATA_DIR/simulations/"${VX:0:2}"_FLWO/CARE_June1425/
     ZENITH_ANGLES=( 00 20 30 35 40 45 50 55 60 65 )
@@ -242,17 +241,17 @@ echo "Wobble offsets: ${WOBBLE_OFFSETS}"
 read_cutlist()
 {
     CUTFILE="${1}"
-    if [[ $CUTFILE == "" ]] || [ ! -f $CUTFILE ]; then
+    if [[ $CUTFILE == "" ]] || [ ! -f "$CUTFILE" ]; then
         echo "Error, cuts list file not found, exiting..." >&2
-        echo $CUTFILE
+        echo "$CUTFILE"
         exit 1
     fi
-    CUTLISTFROMFILE=$(cat $CUTFILE)
+    CUTLISTFROMFILE=$(cat "$CUTFILE")
     CUTLIST=""
     for CUT in "${CUTLISTFROMFILE[@]}"; do
         CUTLIST="${CUTLIST} ANASUM.GammaHadron-Cut-$CUT.dat"
     done
-    echo $CUTLIST
+    echo "$CUTLIST"
 }
 
 # Cut types are used for BDT training and optimisation
@@ -264,7 +263,7 @@ CUTTYPES="NTel2-PointSource-Moderate
 if [[ $ANATYPE = "NN"* ]]; then
     CUTTYPES="NTel2-PointSource-SuperSoft"
 fi
-CUTTYPES=`echo $CUTTYPES |tr '\r' ' '`
+CUTTYPES=$(echo "$CUTTYPES" |tr '\r' ' ')
 CUTTYPES=${CUTTYPES//$'\n'/}
 
 echo "===== Start submission ====="
@@ -371,14 +370,14 @@ for VX in $EPOCH; do
                     "$(dirname "$0")/IRF.trainTMVAforGammaHadronSeparation.sh" \
                                  "${TRAINDIR}" \
                                  "$MVADIR"/"$RUNPAR" \
-                                 "${MVADIR}" BDT ${SIMTYPE} ${VX} "${ATM}"
+                                 "${MVADIR}" BDT "${SIMTYPE}" "${VX}" "${ATM}"
                  # Cut optimization
                  elif [[ $IRFTYPE == "OPTIMIZETMVA" ]]; then
                      echo "OPTIMIZE TMVA $C ${BDTDIR}/BackgroundRates/${VX:0:2}"
                      "$(dirname "$0")/IRF.optimizeTMVAforGammaHadronSeparation.sh" \
                          "${BDTDIR}/BackgroundRates/${VX:0:2}" \
                          "${C/PointSource-/}" \
-                         ${SIMTYPE} ${VX} "${ATM}"
+                         "${SIMTYPE}" "${VX}" "${ATM}"
                  fi
             done
             continue
@@ -388,14 +387,14 @@ for VX in $EPOCH; do
        #################################################
        if [[ $IRFTYPE == "TRAINXGBANGRES" ]]; then
            STEREO_PAR="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/XGB-stereo-parameter.json"
-           IDS=$(jq -r '.zenith[].id' $STEREO_PAR)
+           IDS=$(jq -r '.zenith[].id' "$STEREO_PAR")
            for ZAB in $IDS; do
                # Explicitly remove 0.0 bin
                FIXEDWOBBLE="0.25 0.5 0.75 1.0 1.25 1.5 1.75 2.0"
                FIXEDNSB="160 200 350 450"
                    "$(dirname "$0")/IRF.trainXGBforAngularReconstructionBinned.sh" \
-                       $VX $ATM $ZAB "$FIXEDWOBBLE" "$FIXEDNSB" 0 \
-                       $SIMTYPE $ANATYPE $UUID
+                       "$VX" "$ATM" "$ZAB" "$FIXEDWOBBLE" "$FIXEDNSB" 0 \
+                       "$SIMTYPE" "$ANATYPE" "$UUID"
            done
            continue
        fi
@@ -421,8 +420,8 @@ for VX in $EPOCH; do
                fi
                if [[ $IRFTYPE == "TRAINMVANGRES" ]]; then
                    "$(dirname "$0")/IRF.trainTMVAforAngularReconstruction.sh" \
-                       $VX $ATM $ZA "$FIXEDWOBBLE" "$FIXEDNSB" 0 \
-                       $SIMTYPE $ANATYPE $UUID
+                       "$VX" "$ATM" "$ZA" "$FIXEDWOBBLE" "$FIXEDNSB" 0 \
+                       "$SIMTYPE" "$ANATYPE" "$UUID"
                fi
                continue
             fi
@@ -443,20 +442,20 @@ for VX in $EPOCH; do
                        fi
                        if [[ $IRFTYPE == "EVNDISP" ]]; then
                            "$(dirname "$0")/IRF.evndisp_MC.sh" \
-                               $SIMDIRZA $VX $ATM $ZA $WOBBLE $NOISE \
-                               $SIMTYPE $ACUTS 1 $ANATYPE $UUID
+                               "$SIMDIRZA" "$VX" "$ATM" "$ZA" "$WOBBLE" "$NOISE" \
+                               "$SIMTYPE" $ACUTS 1 "$ANATYPE" "$UUID"
                        elif [[ $IRFTYPE == "EVNDISPCOMPRESS" ]]; then
                            "$(dirname "$0")/IRF.compress_evndisp_MC.sh" \
-                               $SIMDIRZA $VX $ATM $ZA $WOBBLE $NOISE \
-                               $SIMTYPE $ANATYPE $UUID
+                               "$SIMDIRZA" "$VX" "$ATM" "$ZA" "$WOBBLE" "$NOISE" \
+                               "$SIMTYPE" "$ANATYPE" "$UUID"
                        fi
                     ######################
                     # make tables
                     elif [[ $IRFTYPE == "MAKETABLES" ]]; then
                         for ID in $RECID; do
                            "$(dirname "$0")/IRF.generate_lookup_table_parts.sh" \
-                               $VX $ATM $ZA $WOBBLE $NOISE \
-                               $ID $SIMTYPE $ANATYPE $UUID
+                               "$VX" "$ATM" "$ZA" "$WOBBLE" "$NOISE" \
+                               "$ID" "$SIMTYPE" "$ANATYPE" "$UUID"
                         done #recID
                     ######################
                     # analyse table files
@@ -472,8 +471,8 @@ for VX in $EPOCH; do
                                 EFFAREACUTLIST="$CUTSLISTFILE"
                             fi
                             "$(dirname "$0")/IRF.mscw_energy_MC.sh" \
-                                $TFILID $VX $ATM $ZA $WOBBLE $NOISE \
-                                $ID $SIMTYPE $ANATYPE $DISPBDT $EFFAREACUTLIST $UUID
+                                "$TFILID" "$VX" "$ATM" "$ZA" "$WOBBLE" "$NOISE" \
+                                "$ID" "$SIMTYPE" "$ANATYPE" $DISPBDT "$EFFAREACUTLIST" "$UUID"
 			            done #recID
                     ######################
                     # analyse effective areas
@@ -484,9 +483,9 @@ for VX in $EPOCH; do
                             for CUTS in "${CUTLIST[@]}"; do
                                echo "calculate effective areas $CUTS (ID $ID)"
                                "$(dirname "$0")/IRF.generate_effective_area_parts.sh" \
-                                   $CUTS $VX $ATM $ZA $WOBBLE $NOISE \
-                                   $ID $SIMTYPE $ANATYPE \
-                                   $DISPBDT $UUID
+                                   "$CUTS" "$VX" "$ATM" "$ZA" "$WOBBLE" "$NOISE" \
+                                   "$ID" "$SIMTYPE" "$ANATYPE" \
+                                   $DISPBDT "$UUID"
                             done # cuts
                         done #recID
                     fi
diff --git a/scripts/IRF.selectRunsForGammaHadronSeparationTraining.sh b/scripts/IRF.selectRunsForGammaHadronSeparationTraining.sh
index 6cca1bf..6374858 100755
--- a/scripts/IRF.selectRunsForGammaHadronSeparationTraining.sh
+++ b/scripts/IRF.selectRunsForGammaHadronSeparationTraining.sh
@@ -80,7 +80,7 @@ echo "Found ${#FLIST[@]} files to process"
 mkdir -p "${3}"
 
 # Pre-create zenith bin directories for efficiency
-for (( j=0; j < $NZEW; j++ )); do
+for (( j=0; j < NZEW; j++ )); do
     mkdir -p "${TARGETDIR}/Ze_${j}"
 done
 
@@ -113,7 +113,7 @@ do
     fi
 
     # Get run info once and parse into array for efficiency
-    RUNINFO=$($EVNDISPSYS/bin/printRunParameter "${F}.root" -runinfo 2>/dev/null)
+    RUNINFO=$("$EVNDISPSYS"/bin/printRunParameter "${F}.root" -runinfo 2>/dev/null)
     if [[ -z "$RUNINFO" ]]; then
         [[ $VERBOSE -eq 1 ]] && echo "  ERROR: Could not read run info"
         ((SKIPPED++))
@@ -167,7 +167,7 @@ do
 
     # Find zenith bin using numeric comparison (bc for float comparison)
     ZEBIN=0
-    for (( j=0; j < $NZEW; j++ )); do
+    for (( j=0; j < NZEW; j++ )); do
         if (( $(echo "${RUNZENITH} > ${ZEBINARRAY[$j]}" | bc -l) )) && \
            (( $(echo "${RUNZENITH} < ${ZEBINARRAY[$j+1]}" | bc -l) )); then
             ZEBIN=$j
diff --git a/scripts/IRF.trainTMVAforAngularReconstruction.sh b/scripts/IRF.trainTMVAforAngularReconstruction.sh
index 53e09ba..d354c53 100755
--- a/scripts/IRF.trainTMVAforAngularReconstruction.sh
+++ b/scripts/IRF.trainTMVAforAngularReconstruction.sh
@@ -2,11 +2,11 @@
 # submit TMVA training for angular reconstruction
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=47:29:00; h_vmem=16000M; tmpdir_size=100G
 
 # EventDisplay version
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 EVNIRFVERSION="v4N"
 
 if [ $# -lt 8 ]; then
@@ -44,9 +44,8 @@ fi
 
 # Run init script
 if [ -z "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 EPOCH="$1"
 ATM="$2"
@@ -79,8 +78,8 @@ BDTFILE="mvaAngRes_${ZA}deg"
 
 # prepare list of input files
 EVNLIST=$ODIR/${BDTFILE}.list
-rm -f ${EVNLIST}
-touch ${EVNLIST}
+rm -f "${EVNLIST}"
+touch "${EVNLIST}"
 
 check_evndisp_directory()
 {
@@ -100,16 +99,16 @@ check_evndisp_directory()
             exit 1
         fi
     fi
-    echo $INDIR
+    echo "$INDIR"
 }
 
 for W in ${WOBBLE}
 do
     for N in ${NOISE}
     do
-        check_evndisp_directory $W $N
+        check_evndisp_directory "$W" "$N"
         # choose a random file from all files
-        ls -1 $INDIR/*[0-9].root.zst | sort -R | head -n 1 >> ${EVNLIST}
+        find "$INDIR" -maxdepth 1 -name "*[0-9].root.zst" | sort -R | head -n 1 >> "${EVNLIST}"
     done
 done
 echo "FILE LIST: ${EVNLIST}"
@@ -136,13 +135,14 @@ do
 
         # run locally or on cluster
         SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-        SUBC=`eval "echo \"$SUBC\""`
+        SUBC=$(eval "echo \"$SUBC\"")
         if [[ $SUBC == *"ERROR"* ]]; then
-            echo $SUBC
+            echo "$SUBC"
             exit
         fi
         if [[ $SUBC == *qsub* ]]; then
-            JOBID=`$SUBC $FSCRIPT`
+            # shellcheck disable=SC2086
+            JOBID=$($SUBC "$FSCRIPT")
             echo "RUN $RUNNUM: JOBID $JOBID"
         elif [[ $SUBC == *condor* ]]; then
             "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT" "$h_vmem" "$tmpdir_size"
@@ -153,7 +153,8 @@ do
             echo "-------------------------------------------------------------------------------"
             echo
         elif [[ $SUBC == *sbatch* ]]; then
-                $SUBC $FSCRIPT
+                # shellcheck disable=SC2086
+                $SUBC "$FSCRIPT"
         elif [[ $SUBC == *parallel* ]]; then
             echo "$FSCRIPT &> $FSCRIPT.log" >> "$LOGDIR/runscripts.dat"
         fi
diff --git a/scripts/IRF.trainTMVAforGammaHadronSeparation.sh b/scripts/IRF.trainTMVAforGammaHadronSeparation.sh
index 8777f76..72d87a7 100755
--- a/scripts/IRF.trainTMVAforGammaHadronSeparation.sh
+++ b/scripts/IRF.trainTMVAforGammaHadronSeparation.sh
@@ -7,9 +7,9 @@
 # - fixed of NSB levels (adapted to stdHV settings)
 #
 
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:59:59; h_vmem=8000M; tmpdir_size=24G
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 if [ $# -lt 7 ]; then
 echo "
@@ -43,9 +43,8 @@ fi
 
 # Run init script
 if [ -z "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 BDIR="$1"
 RUNPAR="$2"
@@ -85,7 +84,7 @@ if [[ ! -d "$BDIR" ]]; then
 fi
 
 # Check that TMVA run parameter file exists
-if [[ "$RUNPAR" == `basename $RUNPAR` ]]; then
+if [[ "$RUNPAR" == $(basename "$RUNPAR") ]]; then
     RUNPAR="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/$RUNPAR"
 fi
 if [[ ! -f "$RUNPAR" ]]; then
@@ -93,14 +92,14 @@ if [[ ! -f "$RUNPAR" ]]; then
     exit 1
 fi
 
-RXPAR=`basename $RUNPAR .runparameter`
+RXPAR=$(basename "$RUNPAR" .runparameter)
 echo "Original TMVA run parameter file: $RXPAR.runparameter "
 
 LOGDIR="$ODIR/TMVA.ANADATA.${UUID}"
 echo "Output: $ODIR"
 echo "Logs: $LOGDIR"
-mkdir -p $LOGDIR
-mkdir -p $ODIR
+mkdir -p "$LOGDIR"
+mkdir -p "$ODIR"
 
 #####################################
 # Read runparameter file once for efficiency
@@ -112,23 +111,23 @@ if echo "$RUNPAR_CONTENT" | grep -q "^\* ENERGYBINS"; then
     ENBINS=$(echo "$RUNPAR_CONTENT" | grep "^\* ENERGYBINS" | sed -e 's/* ENERGYBINS//' | sed -e 's/ /\n/g')
     mapfile -t EBINARRAY <<< "$ENBINS"
     count1=1
-    NENE=$((${#EBINARRAY[@]}-$count1)) # get number of bins
-    for (( i=0; i < $NENE; i++ ))
+    NENE=$(( ${#EBINARRAY[@]}-count1 )) # get number of bins
+    for (( i=0; i < NENE; i++ ))
     do
-        EBINMIN[$i]=${EBINARRAY[$i]}
-        EBINMAX[$i]=${EBINARRAY[$i+1]}
+        EBINMIN[i]=${EBINARRAY[i]}
+        EBINMAX[i]=${EBINARRAY[i+1]}
     done
 else
     ENBINS=$(echo "$RUNPAR_CONTENT" | grep "^\* ENERGYBINEDGES" | sed -e 's/* ENERGYBINEDGES//' | sed -e 's/ /\n/g')
     mapfile -t EBINARRAY <<< "$ENBINS"
     count1=1
-    NENE=$((${#EBINARRAY[@]}-$count1)) # get number of bins
+    NENE=$(( ${#EBINARRAY[@]}-count1 )) # get number of bins
     z="0"
-    for (( i=0; i < $NENE; i+=2 ))
+    for (( i=0; i < NENE; i+=2 ))
     do
-        EBINMIN[$z]=${EBINARRAY[$i]}
-        EBINMAX[$z]=${EBINARRAY[$i+1]}
-        let "z = ${z} + 1"
+        EBINMIN[z]=${EBINARRAY[i]}
+        EBINMAX[z]=${EBINARRAY[i+1]}
+        (( z++ ))
     done
     NENE=$((${#EBINMAX[@]}))
 fi
@@ -137,7 +136,7 @@ fi
 # zenith angle bins
 ZEBINS=$(echo "$RUNPAR_CONTENT" | grep "^\* ZENBINS " | sed -e 's/* ZENBINS//' | sed -e 's/ /\n/g')
 mapfile -t ZEBINARRAY <<< "$ZEBINS"
-NZEW=$((${#ZEBINARRAY[@]}-$count1)) #get number of bins
+NZEW=$(( ${#ZEBINARRAY[@]}-count1 )) #get number of bins
 
 #####################################
 # zenith angle bins of MC simulation files
@@ -162,33 +161,33 @@ SUBSCRIPT="$(dirname "$0")/helper_scripts/IRF.trainTMVAforGammaHadronSeparation_
 
 ###############################################################
 # loop over all energy/zenith bins and submit a job for each bin
-for (( i=0; i < $NENE; i++ ))
+for (( i=0; i < NENE; i++ ))
 do
    echo "==========================================================================="
    echo " "
-   echo "Energy Bin: $(($i+$count1)) of $NENE: ${EBINMIN[$i]} to ${EBINMAX[$i]} (in log TeV)"
-   for (( j=0; j < $NZEW; j++ ))
+   echo "Energy Bin: $((i+count1)) of $NENE: ${EBINMIN[$i]} to ${EBINMAX[$i]} (in log TeV)"
+   for (( j=0; j < NZEW; j++ ))
    do
       echo "---------------------------------------------------------------------------"
-      echo "Zenith Bin: $(($j+$count1)) of $NZEW: ${ZEBINARRAY[$j]} to ${ZEBINARRAY[$j+1]} (deg)"
+      echo "Zenith Bin: $((j+count1)) of $NZEW: ${ZEBINARRAY[$j]} to ${ZEBINARRAY[$j+1]} (deg)"
 
       # updating the run parameter file for each parameter space
       RFIL=$ODIR/$RXPAR"_$i""_$j"
       echo "TMVA Runparameter file: $RFIL.runparameter"
-      rm -f $RFIL
+      rm -f "$RFIL"
 
-      echo "* ENERGYBINS ${EBINMIN[$i]} ${EBINMAX[$i]}" > $RFIL.runparameter
-      echo "* ZENBINS  ${ZEBINARRAY[$j]} ${ZEBINARRAY[$j+1]}" >> $RFIL.runparameter
-      echo "$RUNPAR_CONTENT" | grep "^\*" | grep -v ENERGYBINS | grep -v ENERGYBINEDGES | grep -v ZENBINS | grep -v OUTPUTFILE | grep -v SIGNALFILE | grep -v BACKGROUNDFILE | grep -v MCXYOFF >> $RFIL.runparameter
+      echo "* ENERGYBINS ${EBINMIN[$i]} ${EBINMAX[$i]}" > "$RFIL".runparameter
+      echo "* ZENBINS  ${ZEBINARRAY[$j]} ${ZEBINARRAY[$j+1]}" >> "$RFIL".runparameter
+      echo "$RUNPAR_CONTENT" | grep "^\*" | grep -v ENERGYBINS | grep -v ENERGYBINEDGES | grep -v ZENBINS | grep -v OUTPUTFILE | grep -v SIGNALFILE | grep -v BACKGROUNDFILE | grep -v MCXYOFF >> "$RFIL".runparameter
 
       nTrainSignal=200000
       nTrainBackground=200000
 
-      echo "* PREPARE_TRAINING_OPTIONS SplitMode=Random:!V:nTrain_Signal=$nTrainSignal:nTrain_Background=$nTrainBackground::nTest_Signal=$nTrainSignal:nTest_Background=$nTrainBackground" >> $RFIL.runparameter
-
-      echo "* OUTPUTFILE ODIR ${ONAME}_${i}_${j}" >> $RFIL.runparameter
-
-      echo "#######################################################################################" >> $RFIL.runparameter
+      {
+          echo "* PREPARE_TRAINING_OPTIONS SplitMode=Random:!V:nTrain_Signal=$nTrainSignal:nTrain_Background=$nTrainBackground::nTest_Signal=$nTrainSignal:nTest_Background=$nTrainBackground"
+          echo "* OUTPUTFILE ODIR ${ONAME}_${i}_${j}"
+          echo "#######################################################################################"
+      } >> "$RFIL.runparameter"
       # signal and background files (depending on on-axis or cone data set)
       # Collect all signal files first, then write in one batch
       {
@@ -223,17 +222,17 @@ do
               done
           fi
           shopt -u nullglob
-      } >> $RFIL.runparameter
-      echo "#######################################################################################" >> $RFIL.runparameter
+      } >> "$RFIL".runparameter
+      echo "#######################################################################################" >> "$RFIL".runparameter
       BLIST="$ODIR/BackgroundRunlist_Ze${j}.list"
-      rm -f ${BLIST}
+      rm -f "${BLIST}"
       if [[ ! -d "${BDIR}/Ze_${j}" ]]; then
           echo "Error, directory with background files ${BDIR}/Ze_${j} not found, exiting..."
           exit 1
       fi
       # Optimized background file listing using awk instead of subshell per file
       # This replaces the get_run_prefix() function call for each file
-      find ${BDIR}/Ze_${j} -name "*.root" -printf "%f\n" | sort -n | \
+      find "${BDIR}"/Ze_${j} -name "*.root" -printf "%f\n" | sort -n | \
       awk '{
           filename = $0;
           # Remove extension to get run number (equivalent to ${1%%.*})
@@ -255,20 +254,21 @@ do
           -e "s|MCDIRECTORY|$SDIR|" \
           -e "s|DATADIRECTORY|$BCKFILEDIR|" \
           -e "s|OUTPUTDIR|${ODIR}|" \
-          -e "s|OUTNAME|$ODIR/$ONAME_${i}_${j}|" $SUBSCRIPT.sh > $FSCRIPT.sh
+          -e "s|OUTNAME|$ODIR/${ONAME}_${i}_${j}|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
-      chmod u+x $FSCRIPT.sh
-      echo $FSCRIPT.sh
+      chmod u+x "$FSCRIPT".sh
+      echo "$FSCRIPT".sh
 
       # run locally or on cluster
       SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
       SUBC=$(eval "echo \"$SUBC\"")
       if [[ $SUBC == *"ERROR"* ]]; then
-            echo $SUBC
+            echo "$SUBC"
             exit
       fi
       if [[ $SUBC == *qsub* ]]; then
-         JOBID=$($SUBC $FSCRIPT.sh)
+         # shellcheck disable=SC2086
+         JOBID=$($SUBC "$FSCRIPT".sh)
          # account for -terse changing the job number format
          if [[ $SUBC != *-terse* ]] ; then
             echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
@@ -284,10 +284,12 @@ do
         echo "-------------------------------------------------------------------------------"
         echo
       elif [[ $SUBC == *sbatch* ]]; then
-            $SUBC $FSCRIPT.sh
+            # shellcheck disable=SC2086
+            $SUBC "$FSCRIPT".sh
       elif [[ $SUBC == *parallel* ]]; then
-         echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.dat
-         cat $LOGDIR/runscripts.dat | $SUBC
+         echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts.dat
+         # shellcheck disable=SC2086
+         cat "$LOGDIR"/runscripts.dat | $SUBC
       elif [[ "$SUBC" == *simple* ]] ; then
          "$FSCRIPT.sh" | tee "$FSCRIPT.log"
       fi
diff --git a/scripts/IRF.trainXGBforAngularReconstructionBinned.sh b/scripts/IRF.trainXGBforAngularReconstructionBinned.sh
index e78b2ab..7864ec0 100755
--- a/scripts/IRF.trainXGBforAngularReconstructionBinned.sh
+++ b/scripts/IRF.trainXGBforAngularReconstructionBinned.sh
@@ -1,10 +1,10 @@
 #!/bin/bash
 # train XGB for angular reconstruction
 
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=47:29:00; h_vmem=16000M; tmpdir_size=100G
 
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 if [ $# -lt 7 ]; then
 echo "
@@ -42,9 +42,8 @@ fi
 
 # Run init script
 if [ -z "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 EPOCH="$1"
 ATM="$2"
@@ -71,13 +70,13 @@ echo "Logs: $LOGDIR"
 
 # prepare list of input files
 MSCWLIST="$ODIR/xgbFiles.list"
-rm -f ${MSCWLIST}
-touch ${MSCWLIST}
+rm -f "${MSCWLIST}"
+touch "${MSCWLIST}"
 
 INDIR="$VERITAS_IRFPRODUCTION_DIR/$EDVERSION/${ANALYSIS_TYPE}/$SIMTYPE/${EPOCH}_ATM${ATM}_gamma/MSCW_RECID${RECID}_DISP"
 
 STEREO_PAR="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/XGB-stereo-parameter.json"
-TRAIN_ANGLES=$(jq -r ".zenith[] | select(.id==\"$ZA\") | .train | join(\" \")" $STEREO_PAR)
+TRAIN_ANGLES=$(jq -r ".zenith[] | select(.id==\"$ZA\") | .train | join(\" \")" "$STEREO_PAR")
 if [[ -z "$TRAIN_ANGLES" ]]; then
     echo "Error: Bin ID $ZA not found in $STEREO_PAR"
     exit 1
@@ -113,13 +112,14 @@ echo "$FSCRIPT"
 
 # run locally or on cluster
 SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-SUBC=`eval "echo \"$SUBC\""`
+SUBC=$(eval "echo \"$SUBC\"")
 if [[ $SUBC == *"ERROR"* ]]; then
-    echo $SUBC
+    echo "$SUBC"
     exit
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT")
     echo "RUN $RUNNUM: JOBID $JOBID"
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT" "$h_vmem" "$tmpdir_size"
@@ -130,7 +130,8 @@ elif [[ $SUBC == *condor* ]]; then
     echo "-------------------------------------------------------------------------------"
     echo
 elif [[ $SUBC == *sbatch* ]]; then
-        $SUBC $FSCRIPT
+        # shellcheck disable=SC2086
+        $SUBC "$FSCRIPT"
 elif [[ $SUBC == *parallel* ]]; then
     echo "$FSCRIPT &> $FSCRIPT.log" >> "$LOGDIR/runscripts.dat"
 fi
diff --git a/scripts/IRF.trainXGBforGammaHadronSeparationTraining.sh b/scripts/IRF.trainXGBforGammaHadronSeparationTraining.sh
index 6c21614..632fbb9 100755
--- a/scripts/IRF.trainXGBforGammaHadronSeparationTraining.sh
+++ b/scripts/IRF.trainXGBforGammaHadronSeparationTraining.sh
@@ -3,9 +3,9 @@
 #
 # - training at wobble offsets 0.5 deg only
 
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:59:59; h_vmem=16000M; tmpdir_size=24G
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 if [ $# -lt 6 ]; then
 echo "
@@ -37,9 +37,8 @@ fi
 
 # Run init script
 if [ -z "$EVNDISP_APPTAINER" ]; then
-    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
+    bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 BDIR="$1"
 RUNPAR="$2"
@@ -77,7 +76,7 @@ if [[ ! -d "$BDIR" ]]; then
 fi
 
 # Check that XGB run parameter file exists
-if [[ "$RUNPAR" == `basename $RUNPAR` ]]; then
+if [[ "$RUNPAR" == $(basename "$RUNPAR") ]]; then
     RUNPAR="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/$RUNPAR"
 fi
 if [[ ! -f "$RUNPAR" ]]; then
@@ -88,14 +87,13 @@ fi
 LOGDIR="$ODIR/XGB.ANADATA.${UUID}"
 echo "Output: $ODIR"
 echo "Logs: $LOGDIR"
-mkdir -p $LOGDIR
-mkdir -p $ODIR
+mkdir -p "$LOGDIR"
+mkdir -p "$ODIR"
 
 #####################################
 # energy / zenith bins
 NENE=$(jq '.energy_bins_log10_tev | length' "$RUNPAR")
 NEZE=$(jq '.zenith_bins_deg | length' "$RUNPAR")
-RUNPAR_CONTENT=$(cat "$RUNPAR")
 echo "Number of energy / zenith bins: $NENE $NEZE"
 
 #####################################
@@ -135,7 +133,7 @@ if [[ ${SIMTYPE:0:5} = "GRISU" ]]; then
 else
     for z in "${ZENITH_ANGLES[@]}"; do
         for n in "${NOISE_VALUES[@]}"; do
-            for f in "$SDIR"/${z}deg_*wob_NOISE${n}.mscw.root; do
+            for f in "$SDIR"/"${z}"deg_*wob_NOISE"${n}".mscw.root; do
 
                 [[ -f "$f" ]] && echo "$f" >> "$SIGNALLIST"
             done
@@ -148,19 +146,19 @@ echo "Background file list: $BCKLIST"
 rm -f "${BCKLIST}"
 touch "${BCKLIST}"
 tmpfile=$(mktemp)
-for ((i=0; i<${NEZE}; i++)); do
+for ((i=0; i<NEZE; i++)); do
   if [[ ! -d "${BDIR}/Ze_${i}" ]]; then
       echo "Error, directory with background files ${BDIR}/Ze_${i} not found, exiting..."
       exit 1
   fi
-  find ${BDIR}/Ze_${i} -name "*.root" | shuf -n 1000 >> "${tmpfile}"
+  find "${BDIR}"/Ze_${i} -name "*.root" | shuf -n 1000 >> "${tmpfile}"
 done
 shuf "$tmpfile" > "${BCKLIST}"
 rm "$tmpfile"
 
 ###############################################################
 # loop over energy bins and submit a job for each bin
-for (( i=0; i < $NENE; i++ )); do
+for (( i=0; i < NENE; i++ )); do
     echo "Energy Bin: $i"
 
     FSCRIPT=$LOGDIR/XGBGAMMA"_$EPOCH""_ENERGY$i.sh"
@@ -168,16 +166,16 @@ for (( i=0; i < $NENE; i++ )); do
         -e "s|MSCWBCK|$BCKLIST|" \
         -e "s|MODELPARA|$RUNPAR|" \
         -e "s|ENERGYBIN|$i|" \
-        -e "s|OUTPUTDIR|${ODIR}|" $SUBSCRIPT > $FSCRIPT
+        -e "s|OUTPUTDIR|${ODIR}|" "$SUBSCRIPT" > "$FSCRIPT"
 
-    chmod u+x $FSCRIPT
-    echo $FSCRIPT
+    chmod u+x "$FSCRIPT"
+    echo "$FSCRIPT"
 
     # run locally or on cluster
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
     SUBC=$(eval "echo \"$SUBC\"")
     if [[ $SUBC == *"ERROR"* ]]; then
-        echo $SUBC
+        echo "$SUBC"
         exit
     fi
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT" "$h_vmem" "$tmpdir_size"
diff --git a/scripts/RUNLIST.findBackgroundRuns.sh b/scripts/RUNLIST.findBackgroundRuns.sh
index e97c622..ab7895d 100755
--- a/scripts/RUNLIST.findBackgroundRuns.sh
+++ b/scripts/RUNLIST.findBackgroundRuns.sh
@@ -56,15 +56,14 @@ exit
 fi
 
 # Run init script
-bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 [[ "$1" ]] && ALLOW_THREE_TEL=$1 || ALLOW_THREE_TEL=0
 [[ "$2" ]] && WORST_WEATHER=$2   || WORST_WEATHER='B'
 [[ "$3" ]] && MIN_DURATION=$3    || MIN_DURATION=15
 [[ "$4" ]] && DATE_BEG="$4"      || DATE_BEG="2011-01-01"
-[[ "$5" ]] && DATE_END="$5"      || DATE_END=`date +"%Y-%m-%d"`
+[[ "$5" ]] && DATE_END="$5"      || DATE_END=$(date +"%Y-%m-%d")
 [[ "$6" ]] && MODE="$6" || MODE="observing"
 [[ "$7" ]] && DQMCATEGORY="$7" || DQMCATEGORY="science"
 [[ "$8" ]] && ELEVSTRING="$8"  || ELEVSTRING=""
@@ -112,7 +111,7 @@ MAXAZIM=$( echo "$AZIMSTRING" | cut -d '-' -f 2 )
 #echo "MAXAZIM:'$MAXAZIM'"
 
 # Get VERITAS database URL from EVNDISP.global.runparameter file
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/EVNDISP.global.runparameter | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 if [ ! -n "$MYSQLDB" ]; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
     exit 1
@@ -121,7 +120,7 @@ MYSQL="mysql -u readonly -h $MYSQLDB -A"
 
 # get segments of time that are within our time, azimuth, and elevation bounts
 #echo "submitting database request..."
-TIMESEGMENTS=$( $EVNDISPSYS/bin/VTS.getObservingTimesWithinTimeAzElBounds "$DATE_BEG" "$DATE_END" "$MINELEV" "$MAXELEV" "$MINAZIM" "$MAXAZIM" | grep -P "^MJDSEGMENT" | awk '{ printf "%s %s\n", $2, $4 }' )
+TIMESEGMENTS=$( "$EVNDISPSYS"/bin/VTS.getObservingTimesWithinTimeAzElBounds "$DATE_BEG" "$DATE_END" "$MINELEV" "$MAXELEV" "$MINAZIM" "$MAXAZIM" | grep -P "^MJDSEGMENT" | awk '{ printf "%s %s\n", $2, $4 }' )
 #echo "TIMESEGMENTS:"
 #echo "$TIMESEGMENTS"
 
@@ -129,7 +128,7 @@ TIMESEGMENTS=$( $EVNDISPSYS/bin/VTS.getObservingTimesWithinTimeAzElBounds "$DATE
 # which runs fall into these time segments
 TIMESEGCONDITION=""
 segmentiter=0
-while read lin ; do
+while read -r lin ; do
   segmentiter=$((segmentiter+1))
   #echo "$segmentiter - lin:'$lin'"
   mjdstart=$( echo "$lin" | cut -d ' ' -f 1 )
diff --git a/scripts/RUNLIST.findDBSourceCoordinates.sh b/scripts/RUNLIST.findDBSourceCoordinates.sh
index 6ebfa0c..1d78307 100755
--- a/scripts/RUNLIST.findDBSourceCoordinates.sh
+++ b/scripts/RUNLIST.findDBSourceCoordinates.sh
@@ -2,15 +2,15 @@
 
 if [ ! "$#" -eq "1" ] || [ "$1" = "-h" ] ; then
 	echo "Print the coordinates of a source" ; echo
-	echo "`basename $0` <sourcename>" ; echo
+	echo "$(basename "$0") <sourcename>" ; echo
 	echo "<source name>  : The name of the source, as stored in VERITAS.tblObserving_Sources"
 	echo "                 or from \$EVNDISPSYS/scripts/VTS/RUNLIST.findDBSourceCoordinates.sh" ; echo
 	echo "Examples:" ; echo
 	echo "  Print the Crab's position:"
-	echo "  $ `basename $0` \"Crab\""
+	echo "  $ $(basename "$0") \"Crab\""
 	echo "  83.633349 22.014475" ; echo
 	echo "  Print Markarian 501's position:"
-	echo "  $ `basename $0` \"Mrk501\""
+	echo "  $ $(basename "$0") \"Mrk501\""
 	echo "  253.467529 39.760300" ; echo
 	echo "Source name should be from the database table VERITAS.tblObserving_Sources ,"
 	echo "Prints the RA/DEC (in degrees, J2000 epoch) of the sourcename, as stored in the database."
@@ -26,7 +26,7 @@ SOURCENAME="$1"
 #echo "Searching for sources that contain '$SOURCENAME'"
 
 # get url of veritas db
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/EVNDISP.global.runparameter | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 if [ ! -n "$MYSQLDB" ] ; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
     exit 1
@@ -39,8 +39,8 @@ while read -r EPOCH RA DEC _; do
 	if [[ "$EPOCH" == "2000" ]] ; then
 		SRCRADEG=$(  bc -l <<< "$RA  * 180.0 / 3.141592" ) # convert radians to degrees
 		SRCDECDEG=$( bc -l <<< "$DEC * 180.0 / 3.141592" )
-		SRCRADEG=$(  printf "%9.6f" $SRCRADEG  )
-		SRCDECDEG=$( printf "%9.6f" $SRCDECDEG )
+		SRCRADEG=$(  printf "%9.6f" "$SRCRADEG"  )
+		SRCDECDEG=$( printf "%9.6f" "$SRCDECDEG" )
 		echo "$SRCRADEG $SRCDECDEG"
 		exit 0
 	fi
diff --git a/scripts/RUNLIST.findDBSourceNames.sh b/scripts/RUNLIST.findDBSourceNames.sh
index 8f1c6c9..ab6d35b 100755
--- a/scripts/RUNLIST.findDBSourceNames.sh
+++ b/scripts/RUNLIST.findDBSourceNames.sh
@@ -41,15 +41,14 @@ exit
 fi
 
 # Run init script
-bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 SEARCHSTR="$1"
 echo "Searching for sources that contain '$SEARCHSTR'"
 
 # get url of veritas db
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/EVNDISP.global.runparameter | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 if [ ! -n "$MYSQLDB" ] ; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
     exit 1
diff --git a/scripts/RUNLIST.generate.sh b/scripts/RUNLIST.generate.sh
index cf6c60d..a8b3984 100755
--- a/scripts/RUNLIST.generate.sh
+++ b/scripts/RUNLIST.generate.sh
@@ -45,8 +45,7 @@ exit
 fi
 
 # Run init script
-bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 SOURCE_NAME=$1
@@ -78,7 +77,7 @@ for (( i=0; i < ${#WEATHER_GRADES[@]}; i++ )); do
 done
 
 # Get VERITAS database URL from EVNDISP.global.runparameter file
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/EVNDISP.global.runparameter | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 if [ ! -n "$MYSQLDB" ]; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
     exit 1
diff --git a/scripts/RUNLIST.preprocessing.sh b/scripts/RUNLIST.preprocessing.sh
index 3a3c653..70fce6c 100755
--- a/scripts/RUNLIST.preprocessing.sh
+++ b/scripts/RUNLIST.preprocessing.sh
@@ -24,8 +24,7 @@ exit
 fi
 
 # Run init script
-bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 [[ "$1" ]] && START_DATE=$1" 00:00:00" || START_DATE="2011-01-01 00:00:00"
@@ -41,7 +40,7 @@ TEL_MASKS="('15', '7', '11', '13', '14')"
 TEL_CUT_MASKS="('0', '8', '4', '2', '1')"
 
 # Get VERITAS database URL from EVNDISP.global.runparameter file
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/EVNDISP.global.runparameter | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 if [ ! -n "$MYSQLDB" ]; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
     exit 1
diff --git a/scripts/RUNLIST.whichRunsAreArrayEpoch.sh b/scripts/RUNLIST.whichRunsAreArrayEpoch.sh
index 95bf5d4..09c541b 100755
--- a/scripts/RUNLIST.whichRunsAreArrayEpoch.sh
+++ b/scripts/RUNLIST.whichRunsAreArrayEpoch.sh
@@ -3,19 +3,19 @@
 
 #echo "\$#:$#   \$1:$1   \$2:$2   \$3:$3   \$4:$4"
 
-ISPIPEFILE=`readlink /dev/fd/0` # check to see if input is from terminal, or from a pipe
+ISPIPEFILE=$(readlink /dev/fd/0) # check to see if input is from terminal, or from a pipe
 #echo "\$ISPIPEFILE: '$ISPIPEFILE'"
 if [[ "$ISPIPEFILE" =~ ^/dev/pts/[0-9]{1,2} ]] ; then # its a terminal (not a pipe)
 	if ! [ $# -eq 2 ] ; then # the human didn't add any arguments, and we must tell them so
 		echo "Prints the run numbers that are of the specific run versions runs."
 		echo "  for just V4 runs, do"
-		echo "    $ `basename $0` 4 <file of runs>"
+		echo "    $ $(basename "$0") 4 <file of runs>"
 		echo "  for just V5 runs, do"
-		echo "    $ `basename $0` 5 <file of runs>"
+		echo "    $ $(basename "$0") 5 <file of runs>"
 		echo "  for just V6_2014 and V6_2015 (scaling tests, do not use in production) runs, do"
-		echo "    $ `basename $0` 6_2014,6_2015 <file of runs>"
+		echo "    $ $(basename "$0") 6_2014,6_2015 <file of runs>"
 		echo "  to print all V5 and V6 runs, do"
-		echo "    $ `basename $0` 5,6 <file of runs>"
+		echo "    $ $(basename "$0") 5,6 <file of runs>"
 		exit
 	fi
 fi
@@ -24,11 +24,11 @@ INPUTEPOCH="$1"
 
 # list of run_id's to read in
 RUNFILE=$2
-if [ ! -e $RUNFILE ] ; then
+if [ ! -e "$RUNFILE" ] ; then
 	echo "File $RUNFILE could not be found in $PWD , sorry."
 	exit
 fi
-RUNLIST=`cat $RUNFILE`
+RUNLIST=$(cat "$RUNFILE")
 #echo "RUNLIST:$RUNLIST"
 
 # how should we get the array epochs?
@@ -40,7 +40,7 @@ if [[ "$METHOD" == "irfperiod" ]]; then
     PARAMFILE="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/VERITAS.Epochs.runparameter"
 
     # get only lines that start with '*'
-    EPOCHTHRESH=$( cat $PARAMFILE | grep -P "^\s??\*" | grep "EPOCH" | grep -P "V\d" )
+    EPOCHTHRESH=$( cat "$PARAMFILE" | grep -P "^\s??\*" | grep "EPOCH" | grep -P "V\d" )
     AVAILABLEEPOCHS=$( echo "$EPOCHTHRESH" | awk '{ print $3 }' )
     DESIREDPERIODS=$( echo "$INPUTEPOCH" | sed 's/\,/ /g' | sed 's/\;/ /g' | tr " " "\n" )
     # loop over runs in runlist
@@ -69,7 +69,7 @@ if [[ "$METHOD" == "useparamfile" ]] ; then
 	PARAMFILE="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/VERITAS.Epochs.runparameter"
 
 	# get only lines that start with '*'
-	EPOCHTHRESH=$( cat $PARAMFILE | grep -P "^\s??\*" | grep "EPOCH" | grep -P "V\d" )
+	EPOCHTHRESH=$( cat "$PARAMFILE" | grep -P "^\s??\*" | grep "EPOCH" | grep -P "V\d" )
 	#echo "$EPOCHTHRESH"
 
 	# find out what are the smallest and largest epochs to work with
@@ -85,7 +85,7 @@ if [[ "$METHOD" == "useparamfile" ]] ; then
 	for run in $RUNLIST ; do
 
 		# loop through all epochs between min and max
-		for epoch in $(seq $MINEPOCH $MAXEPOCH) ; do
+		for epoch in $(seq "$MINEPOCH" "$MAXEPOCH") ; do
 
 			# check to see if the user wants each epoch
 			if [[ $INPUTEPOCH == *$epoch* ]] ; then
diff --git a/scripts/RUNLIST.whichRunsAreAtmosphere.sh b/scripts/RUNLIST.whichRunsAreAtmosphere.sh
index a78035e..7bdb592 100755
--- a/scripts/RUNLIST.whichRunsAreAtmosphere.sh
+++ b/scripts/RUNLIST.whichRunsAreAtmosphere.sh
@@ -2,18 +2,18 @@
 # from a run list, prints the list of runs that were taken in a specific atmosphere, summer(22/62) or winter(21/61)
 
 # check to see if input is from terminal, or from a pipe
-ISPIPEFILE=`readlink /dev/fd/0`
+ISPIPEFILE=$(readlink /dev/fd/0)
 if [[ "$ISPIPEFILE" =~ ^/dev/pts/[0-9]{1,2} && $# -lt 2 ]]; then # its a terminal (not a pipe)
     echo
     echo "From a runlist or pipe, prints the run numbers that are of a particular atmosphere."
-    echo " $ `basename $0` [w|21|s|22] <file of runs>" ; echo
+    echo " $ $(basename "$0") [w|21|s|22] <file of runs>" ; echo
     echo "w = 21 = 61 = winter, s = 22 = 62 = summer" ; echo
     echo "Print list of summer runs:"
-    echo " $ `basename $0` s myrunlist.dat" ; echo
+    echo " $ $(basename "$0") s myrunlist.dat" ; echo
     echo "Print list of winter runs:"
-    echo " $ `basename $0` 61 myrunlist.dat" ; echo
+    echo " $ $(basename "$0") 61 myrunlist.dat" ; echo
     echo "Works with pipes : "
-    echo " $ cat myrunlist.dat | `basename $0` w" ; echo
+    echo " $ cat myrunlist.dat | $(basename "$0") w" ; echo
     echo "Summer/winter transition dates taken from $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/VERITAS.Epochs.runparameter"
     exit
 fi
@@ -22,16 +22,16 @@ function echoerr(){ echo "$@" 1>&2; } #for spitting out error text
 
 # list of run_id's to read in
 RUNFILE=$2
-if [ ! -e $RUNFILE ] ; then
+if [ ! -e "$RUNFILE" ] ; then
 	echo "File $RUNFILE could not be found in $PWD , sorry."
 	exit
 fi
-RUNLIST=`cat $RUNFILE`
+RUNLIST=$(cat "$RUNFILE")
 #echo "RUNLIST:$RUNLIST"
 
 SUMMFLAG=false
 WINTFLAG=false
-LOWARG=`echo "$1" | tr '[A-Z]' '[a-z]'` # make all uppercase letters in arg 1 lowercase, for easier handling
+LOWARG=$(echo "$1" | tr '[:upper:]' '[:lower:]') # make all uppercase letters in arg 1 lowercase, for easier handling
 #echo "\$LOWARG: '$LOWARG'"
 if [[ "$LOWARG" == *w* ]] || [[ "$LOWARG" == "21" ]] || [[ "$LOWARG" == "61" ]] ; then
 	WINTFLAG=true
@@ -73,9 +73,7 @@ function IsWinter {
 		local ATMOCODE=""
 		local MINDATE=""
 		local MAXDATE=""
-		(IFS='
-'
-		for line in $ATMOTHRESH ; do
+		while IFS= read -r line ; do
 			#echoerr "line:$line"
 			ATMOCODE=$( echo "$line" | awk '{ print $3 }' | grep -oP "\d+" )
 			MINDATE=$(  echo "$line" | awk '{ print $4 }' | tr -d '-' | grep -oP "\d+" )
@@ -99,8 +97,7 @@ function IsWinter {
 					break
 				fi
 			fi
-		done
-		)
+		done <<< "$ATMOTHRESH"
 		# 3 = did not find valid atmo range
 		if [ ! $FOUNDATMO ] ; then
 			echo 3
@@ -142,7 +139,7 @@ function badAtmosphere {
 }
 
 # get database url from parameter file
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter" | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter" | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 
 if [ ! -n "$MYSQLDB" ] ; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
@@ -158,7 +155,7 @@ MYSQL="mysql -u readonly -h $MYSQLDB -A"
 COUNT=0
 SUB=""
 for ARUN in $RUNLIST ; do
-	if (( $ARUN > 0 )); then
+	if (( ARUN > 0 )); then
 		if [[ "$COUNT" -eq 0 ]] ; then
 			SUB="run_id = $ARUN"
 		else
@@ -180,7 +177,7 @@ while read -r RUNID RUNDATE ; do
 		#echo "  YEARMONTHDAY:$YY$MM$DD"
 
 		# get the atmosphere code
-        STATUSFLAG=`IsWinter "$YY$MM$DD"`
+        STATUSFLAG=$(IsWinter "$YY$MM$DD")
 		#echo "$RUNID '$STATUSFLAG'"
 
 		# did the user ask for summer runs?
diff --git a/scripts/RUNLIST.whichRunsAreObservingMode.sh b/scripts/RUNLIST.whichRunsAreObservingMode.sh
index c840949..f53d569 100755
--- a/scripts/RUNLIST.whichRunsAreObservingMode.sh
+++ b/scripts/RUNLIST.whichRunsAreObservingMode.sh
@@ -2,15 +2,15 @@
 # from a run list, prints the list of runs that were taken in a specific observing mode (observing, obsLowHV, obsFilter,...)
 #
 
-ISPIPEFILE=`readlink /dev/fd/0` # check to see if input is from terminal, or from a pipe
+ISPIPEFILE=$(readlink /dev/fd/0) # check to see if input is from terminal, or from a pipe
 if [[ "$ISPIPEFILE" =~ ^/dev/pts/[0-9]{1,2} ]] ; then # its a terminal (not a pipe)
 	if ! [ $# -eq 2 ] ; then # the human didn't add any arguments, and we must tell them so
 		echo
 		echo "From a runlist or pipe, prints the run numbers that have been taken in a particular observing mode."
 		echo "Usage: "
-		echo " $ `basename $0` <mode> <file of runs>"
+		echo " $ $(basename "$0") <mode> <file of runs>"
 		echo "or"
-		echo " $ cat myrunlist.dat | `basename $0` <mode>" ; echo
+		echo " $ cat myrunlist.dat | $(basename "$0") <mode>" ; echo
 		echo "   <mode> = observing for regular runs"
 		echo "            obsLowHV for runs taken with reduced HV"
 		echo "            obsFilter for runs taken with UV filters"
@@ -23,17 +23,17 @@ fi
 
 # list of run_ids to read in
 RUNFILE=$2
-if [ ! -e $RUNFILE ] ; then
+if [ ! -e "$RUNFILE" ] ; then
 	echoerr "File $RUNFILE could not be found in $PWD , sorry."
 	exit 1
 fi
-RUNLIST=`cat $RUNFILE`
+RUNLIST=$(cat "$RUNFILE")
 #echo "RUNLIST:$RUNLIST"
 
 MODE="$1"
 
 # get database url from parameter file
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter" | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter" | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 
 if [ ! -n "$MYSQLDB" ] ; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
@@ -49,7 +49,7 @@ MYSQL="mysql -u readonly -h $MYSQLDB -A"
 COUNT=0
 SUB=""
 for ARUN in $RUNLIST ; do
-	if (( $ARUN > 0 )); then
+	if (( ARUN > 0 )); then
 		if [[ "$COUNT" -eq 0 ]] ; then
 			SUB="run_id = $ARUN"
 		else
diff --git a/scripts/RUNLIST.whichRunsAreOnDisk.sh b/scripts/RUNLIST.whichRunsAreOnDisk.sh
index 5a41b72..8e27741 100755
--- a/scripts/RUNLIST.whichRunsAreOnDisk.sh
+++ b/scripts/RUNLIST.whichRunsAreOnDisk.sh
@@ -6,10 +6,10 @@ DATFLAG=false # flat to print full date of run
 HELPFLAG=false # if true, print help text and exit
 PRINTPATH=false # if true, print full path of file on disl
 DOWNLOADFLAG=true
-RAWDATASERVER=$(grep "\* VTSRAWDATA" $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter  | awk '{print $3}')
-#echo "INP:'`basename $0`' '$1' '$2' '$3'"
+RAWDATASERVER=$(grep "\* VTSRAWDATA" "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/EVNDISP.global.runparameter  | awk '{print $3}')
+#echo "INP:'$(basename $0)' '$1' '$2' '$3'"
 
-ISPIPEFILE=`readlink /dev/fd/0` # check to see if input is from terminal, or from a pipe
+ISPIPEFILE=$(readlink /dev/fd/0) # check to see if input is from terminal, or from a pipe
 if [[ "$ISPIPEFILE" =~ ^/dev/pts/[0-9]{1,2} ]] ; then # its a terminal (not a pipe)
 	if [ "$#" -eq "1" ] ; then # format is "exe <fname>"
 		RUNFILE=$1
@@ -21,7 +21,7 @@ if [[ "$ISPIPEFILE" =~ ^/dev/pts/[0-9]{1,2} ]] ; then # its a terminal (not a pi
 			PRINTPATH=true
 			RUNFILE=$2
 		else
-			echo " Error: `basename $0` doesn't understand flag $1.  Only acceptable flag is -n"
+			echo " Error: $(basename "$0") doesn't understand flag $1.  Only acceptable flag is -n"
 			HELPFLAG=true
 		fi
 	else
@@ -42,7 +42,7 @@ else # it is a pipe
             DATFLAG=true
 			RUNFILE=$2
 		else
-			echo " Error: `basename $0` doesn't understand flag $1.  Only acceptable flag is -n"
+			echo " Error: $(basename "$0") doesn't understand flag $1.  Only acceptable flag is -n"
 			HELPFLAG=true
 		fi
 	else
@@ -54,13 +54,13 @@ fi
 if $HELPFLAG ; then
 	echo
 	echo "Prints the run numbers that ARE stored on disk." ; echo
-	echo " $ `basename $0` <file of runs>" ; echo
+	echo " $ $(basename "$0") <file of runs>" ; echo
 	echo "Prints the full path of runs that ARE stored on disk." ; echo
-	echo " $ `basename $0` -p <file of runs>" ; echo
+	echo " $ $(basename "$0") -p <file of runs>" ; echo
 	echo "Prints the run numbers that are NOT stored on disk" ; echo
-	echo " $ `basename $0` -n <file of runs>" ; echo
-	echo " $ cat <file of runs> | `basename $0`" ; echo
-	echo " $ cat <file of runs> | `basename $0` -n" ; echo
+	echo " $ $(basename "$0") -n <file of runs>" ; echo
+	echo " $ cat <file of runs> | $(basename "$0")" ; echo
+	echo " $ cat <file of runs> | $(basename "$0") -n" ; echo
 	exit
 fi
 
@@ -68,11 +68,11 @@ fi
 
 # list of run_id's to read in
 #RUNFILE=$1
-if [ ! -e $RUNFILE ] ; then
+if [ ! -e "$RUNFILE" ] ; then
 	echo "File '$RUNFILE' could not be found, sorry."
 	exit
 fi
-RUNLISTTMP=`cat $RUNFILE`
+RUNLISTTMP=$(cat "$RUNFILE")
 RUNLIST=$(echo "$RUNLISTTMP" | grep -oP "^\d+$" )
 if [ -z "$RUNLIST" ] ; then
   >&2 echo "Error, RUNLIST.whichRunsAreOnDisk.sh : input file/pipe $RUNLISTTMP contains no runs, exiting..."
@@ -82,7 +82,7 @@ fi
 #echo "Files not on disk:"
 
 # find the veritas db url
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/EVNDISP.global.runparameter | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 if [ ! -n "$MYSQLDB" ] ; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
     exit
@@ -96,7 +96,7 @@ MYSQL="mysql -u readonly -h $MYSQLDB -A"
 COUNT=0
 SUB=""
 for ARUN in $RUNLIST ; do
-	if (( $ARUN > 0 )); then
+	if (( ARUN > 0 )); then
 		if [[ "$COUNT" -eq 0 ]] ; then
 			SUB="run_id = $ARUN"
 		else
@@ -122,7 +122,7 @@ while read -r RUNID RUNDATE ; do
 
 		# test to see if the file exists
 		#echo "  Does file exist: $TARGFILE"
-		if [ -e $TARGFILE ] ; then # file exists
+		if [ -e "$TARGFILE" ] ; then # file exists
 			if ! $NOTFLAG ; then # $NOTFLAG is false, and we should print the runnumber
                 if $PRINTPATH ; then
                     echo "$TARGFILE"
diff --git a/scripts/RUNLIST.whichRunsAreSource.sh b/scripts/RUNLIST.whichRunsAreSource.sh
index 007aac3..90da887 100755
--- a/scripts/RUNLIST.whichRunsAreSource.sh
+++ b/scripts/RUNLIST.whichRunsAreSource.sh
@@ -1,16 +1,11 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # from a run list, prints the list of runs that target a specific source
 
-# variables for coloring terminal output
-CONORM="\e[0m"
-CORED='\e[1;31m'
-
 NOTFLAG=false # flag for if the -n flag was used
 HELPFLAG=false # if true, print help text and exit
 
 # check to see if input is from terminal, or from a pipe
-ISPIPEFILE=`readlink /dev/fd/0`
+ISPIPEFILE=$(readlink /dev/fd/0)
 if [[ "$ISPIPEFILE" =~ ^/dev/pts/[0-9]{1,2} ]] ; then # its a terminal (not a pipe)
 	if [ "$#" -eq "1" ] ; then
 		NOTFLAG=true
@@ -25,7 +20,7 @@ if [[ "$ISPIPEFILE" =~ ^/dev/pts/[0-9]{1,2} ]] ; then # its a terminal (not a pi
 			SOURCE="$2"
 			RUNFILE="$3"
 		else
-			echo " Error: `basename $0` doesn't understand flag '$1'.  Only acceptable flag is -n"
+			echo " Error: $(basename "$0") doesn't understand flag '$1'.  Only acceptable flag is -n"
 			HELPFLAG=true
 		fi
 	else
@@ -46,7 +41,7 @@ else # it is a pipe
 			SOURCE=$2
 			RUNFILE=$3
 		else
-			echo " Error: `basename $0` doesn't understand flag '$1'.  Only acceptable flag is -n"
+			echo " Error: $(basename "$0") doesn't understand flag '$1'.  Only acceptable flag is -n"
 			HELPFLAG=true
 		fi
 	else
@@ -59,7 +54,7 @@ if $HELPFLAG ; then
     echo
     echo "Prints the source names for a list of run numbers,"
 	echo "  OR, only print runs that do or do not target a particular source." ; echo
-    echo "$ `basename $0` [-n] [source name] <file of runs>" ; echo
+    echo "$ $(basename "$0") [-n] [source name] <file of runs>" ; echo
 	echo "Required arguments:"
 	echo "  <file of runs> : The runlist file, containing the list of runs, 1 runnumber per line"
 	echo "                   Can also take input from a piped runlist" ; echo
@@ -69,45 +64,43 @@ if $HELPFLAG ; then
 	echo "                   (only has effect if [source name] is specified)" ; echo
 	echo "Examples:" ; echo
 	echo "  Print source names for each run:"
-	echo "  $ `basename $0` myrunlist.dat"
+	echo "  $ $(basename "$0") myrunlist.dat"
 	echo "  43744 PSRJ2229+6114"
 	echo "  43745 PSRJ2229+6114"
 	echo "  47146 Tycho"
 	echo "  47147 Tycho"
 	echo "  47478 Tycho" ; echo
     echo "  Only print the Tycho runs from a runlist:"
-    echo "  $ `basename $0` \"Tycho\" myrunlist.dat"
+    echo "  $ $(basename "$0") \"Tycho\" myrunlist.dat"
 	echo "  47146"
 	echo "  47147"
 	echo "  47478" ; echo
     echo "  Only print the PSRJ2229+6114 runs from a runlist:"
-    echo "  $ `basename $0` \"PSRJ2229+6114\" myrunlist.dat"
+    echo "  $ $(basename "$0") \"PSRJ2229+6114\" myrunlist.dat"
 	echo "  43744"
 	echo "  43745" ; echo
 	echo "  Print list of non-Tycho runs, along with their source name:"
-	echo "  $ `basename $0` -n \"Tycho\" myrunlist.dat"
+	echo "  $ $(basename "$0") -n \"Tycho\" myrunlist.dat"
 	echo "  43744 PSRJ2229+6114"
 	echo "  43745 PSRJ2229+6114" ; echo
     echo "Works with pipes : "
-    echo "  $ cat myrunlist.dat | `basename $0` \"Tycho\""
+    echo "  $ cat myrunlist.dat | $(basename "$0") \"Tycho\""
 	echo "  47146"
 	echo "  47147"
 	echo "  47478" ; echo
     exit
 fi
 
-function echoerr(){ echo "$@" 1>&2; } #for spitting out error text
-
 # list of run_id's to read in
-if [ ! -e $RUNFILE ] ; then
+if [ ! -e "$RUNFILE" ] ; then
 	echo "File '$RUNFILE' could not be found in $PWD , sorry."
 	exit
 fi
-RUNLIST=`cat $RUNFILE`
+RUNLIST=$(cat "$RUNFILE")
 #echo "RUNLIST:$RUNLIST"
 
 # get database url from parameter file
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter" | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter" | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 
 if [ ! -n "$MYSQLDB" ] ; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
@@ -123,7 +116,7 @@ MYSQL="mysql -u readonly -h $MYSQLDB -A"
 COUNT=0
 SUB=""
 for ARUN in $RUNLIST ; do
-	if (( $ARUN > 0 )); then
+	if (( ARUN > 0 )); then
 		if [[ "$COUNT" -eq 0 ]] ; then
 			SUB="run_id = $ARUN"
 		else
diff --git a/scripts/RUNLIST.whichRunsAreWobble.sh b/scripts/RUNLIST.whichRunsAreWobble.sh
index bfb0592..68d8c31 100755
--- a/scripts/RUNLIST.whichRunsAreWobble.sh
+++ b/scripts/RUNLIST.whichRunsAreWobble.sh
@@ -4,18 +4,18 @@
 CONORM="\e[0m"
 CORED='\e[1;31m'
 
-ISPIPEFILE=`readlink /dev/fd/0` # check to see if input is from terminal, or from a pipe
+ISPIPEFILE=$(readlink /dev/fd/0) # check to see if input is from terminal, or from a pipe
 if [[ "$ISPIPEFILE" =~ ^/dev/pts/[0-9]{1,2} ]] ; then # its a terminal (not a pipe)
 	if ! [ $# -eq 2 ] ; then # the human didn't add any arguments, and we must tell them so
 		echo
 		echo "From a runlist or pipe, prints the run numbers that are of a particular wobble or wobbles."
-		echo " $ `basename $0` [nsew] <file of runs>" ; echo
+		echo " $ $(basename "$0") [nsew] <file of runs>" ; echo
 		echo "Print list of only north wobble runs:"
-		echo " $ `basename $0` n myrunlist.dat" ; echo
+		echo " $ $(basename "$0") n myrunlist.dat" ; echo
 		echo "Print list of only south and east wobble runs:"
-		echo " $ `basename $0` se myrunlist.dat" ; echo
+		echo " $ $(basename "$0") se myrunlist.dat" ; echo
 		echo "Works with pipes : "
-		echo " $ cat myrunlist.dat | `basename $0` w" ; echo
+		echo " $ cat myrunlist.dat | $(basename "$0") w" ; echo
 		exit
 	fi
 fi
@@ -24,11 +24,11 @@ function echoerr(){ echo -e "${CORED}$*${CONORM}" 1>&2; } #for spitting out erro
 
 # list of run_id's to read in
 RUNFILE=$2
-if [ ! -e $RUNFILE ] ; then
+if [ ! -e "$RUNFILE" ] ; then
 	echoerr "File $RUNFILE could not be found in $PWD , sorry."
 	exit 1
 fi
-RUNLIST=`cat $RUNFILE`
+RUNLIST=$(cat "$RUNFILE")
 #echo "RUNLIST:$RUNLIST"
 
 NORTFLAG=false
@@ -36,7 +36,7 @@ SOUTFLAG=false
 EASTFLAG=false
 WESTFLAG=false
 
-LOWARG=`echo "$1" | tr '[A-Z]' '[a-z]'` # make all uppercase letters in arg 1 lowercase, for easier handling
+LOWARG=$(echo "$1" | tr '[:upper:]' '[:lower:]') # make all uppercase letters in arg 1 lowercase, for easier handling
 #echo "\$LOWARG: '$LOWARG'"
 if [[ "$LOWARG" == *n* ]] ; then NORTFLAG=true ; fi
 if [[ "$LOWARG" == *s* ]] ; then SOUTFLAG=true ; fi
@@ -44,7 +44,7 @@ if [[ "$LOWARG" == *e* ]] ; then EASTFLAG=true ; fi
 if [[ "$LOWARG" == *w* ]] ; then WESTFLAG=true ; fi
 
 # get database url from parameter file
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter" | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter" | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 
 if [ ! -n "$MYSQLDB" ] ; then
     echo "* DBSERVER param not found in \$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/EVNDISP.global.runparameter!"
@@ -60,7 +60,7 @@ MYSQL="mysql -u readonly -h $MYSQLDB -A"
 COUNT=0
 SUB=""
 for ARUN in $RUNLIST ; do
-	if (( $ARUN > 0 )); then
+	if (( ARUN > 0 )); then
 		if [[ "$COUNT" -eq 0 ]] ; then
 			SUB="run_id = $ARUN"
 		else
diff --git a/scripts/SPANALYSIS.evndisp_laser_run.sh b/scripts/SPANALYSIS.evndisp_laser_run.sh
index 0597ad8..becbc68 100755
--- a/scripts/SPANALYSIS.evndisp_laser_run.sh
+++ b/scripts/SPANALYSIS.evndisp_laser_run.sh
@@ -31,8 +31,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 RUNNUM=$1
@@ -50,26 +49,38 @@ fi
 CALIBDIR="$VERITAS_USER_DATA_DIR/"
 
 # Check if source vbf file exists
-SF=`find -L $VERITAS_DATA_DIR/data -name "$RUNNUM.cvbf"`
+SF=$(find -L "$VERITAS_DATA_DIR"/data -name "$RUNNUM.cvbf")
 if [ ${#SF} = 0 ]; then
     echo "ERROR: VERITAS source (VBF laser/flasher) file $RUNNUM.cvbf not found in $VERITAS_DATA_DIR/data/"
     exit 1
 fi
 
 # Run options
-OPT="-runmode=$RUNMODE -runnumber=$RUNNUM -lasermin=$LASERMIN -calibrationsumwindow=18 -calibrationsumfirst=2 -reconstructionparameter EVNDISP.reconstruction.SW18_noDoublePass.runparameter -calibrationdirectory $CALIBDIR -writeextracalibtree -printdeadpixelinfo"
+OPT=(
+    "-runmode=$RUNMODE"
+    "-runnumber=$RUNNUM"
+    "-lasermin=$LASERMIN"
+    -calibrationsumwindow=18
+    -calibrationsumfirst=2
+    -reconstructionparameter
+    EVNDISP.reconstruction.SW18_noDoublePass.runparameter
+    -calibrationdirectory
+    "$CALIBDIR"
+    -writeextracalibtree
+    -printdeadpixelinfo
+)
 
 # calculate pedestals (for high gain only)
 if [[ $RUNMODE == 2 ]]; then
     echo "Calculating pedestals for run $RUNNUM"
-    "$(dirname "$0")/SPANALYSIS.evndisp_pedestal_events.sh" $RUNNUM
+    "$(dirname "$0")/SPANALYSIS.evndisp_pedestal_events.sh" "$RUNNUM"
 fi
 
 # calculate gains, looping over all telescopes
-TELTOANA=`echo $TELTOANA | fold -w1`
+TELTOANA=$(echo "$TELTOANA" | fold -w1)
 for i in $TELTOANA; do
     echo "Calculating gains for run $RUNNUM, telescope $i"
-    $EVNDISPSYS/bin/evndisp -teltoana=$i $OPT
+    "$EVNDISPSYS"/bin/evndisp -teltoana="$i" "${OPT[@]}"
 done
 
 exit
diff --git a/scripts/SPANALYSIS.evndisp_laser_runs_from_calibfile.sh b/scripts/SPANALYSIS.evndisp_laser_runs_from_calibfile.sh
index 9f362ba..d39f1c0 100755
--- a/scripts/SPANALYSIS.evndisp_laser_runs_from_calibfile.sh
+++ b/scripts/SPANALYSIS.evndisp_laser_runs_from_calibfile.sh
@@ -19,8 +19,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 CALIBFILE=$1
@@ -28,17 +27,17 @@ CALIBFILE=$1
 # locations of vbf files
 DDIR="$VERITAS_DATA_DIR/data/"
 
-FILES=`grep LASER $CALIBFILE | awk '{print $2"_"$3}'`
+FILES=$(grep LASER "$CALIBFILE" | awk '{print $2"_"$3}')
 
 for AFILE in $FILES
 do
     RUN=${AFILE:0:5}
     DTEL=${AFILE:6}
-    echo $AFILE $RUN $DTEL
-    DFILE=`find -L $DDIR -name "$RUN.cvbf"`
+    echo "$AFILE" "$RUN" "$DTEL"
+    DFILE=$(find -L "$DDIR" -name "$RUN.cvbf")
 
     if [[ -f $DFILE ]]; then
-        "$(dirname "$0")/SPANALYSIS.evndisp_laser_run.sh" $DTEL $DFILE
+        "$(dirname "$0")/SPANALYSIS.evndisp_laser_run.sh" "$DTEL" "$DFILE"
     else
 	    echo "Missing laser/flasher file $DFILE, please download it"
     fi
diff --git a/scripts/SPANALYSIS.evndisp_laser_runs_from_runlist.sh b/scripts/SPANALYSIS.evndisp_laser_runs_from_runlist.sh
index d263325..825ec24 100755
--- a/scripts/SPANALYSIS.evndisp_laser_runs_from_runlist.sh
+++ b/scripts/SPANALYSIS.evndisp_laser_runs_from_runlist.sh
@@ -26,13 +26,12 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 RLIST=$1
 [[ "$2" ]] && TELTOANA=$2 || TELTOANA="1234"
-TELTOANA=`echo $TELTOANA | fold -w1`
+TELTOANA=$(echo "$TELTOANA" | fold -w1)
 
 # locations of vbf files and laser/flasher calibration files
 DDIR="$VERITAS_DATA_DIR/data/"
@@ -43,19 +42,19 @@ if [[ ! -f "$RLIST" ]]; then
     echo "Error, runlist $RLIST not found, exiting..."
     exit 1
 fi
-RUNNUMS=`cat $RLIST`
+RUNNUMS=$(cat "$RLIST")
 
 for RUN in $RUNNUMS; do
     for i in $TELTOANA; do
-        RUN=`$EVNDISPSYS/bin/VTS.getLaserRunFromDB $i $RUN`
+        RUN=$("$EVNDISPSYS"/bin/VTS.getLaserRunFromDB "$i" "$RUN")
         echo "Checking telescope $i, laser run $RUN, data run $RUN:"
         echo "$CALIBDIR/Tel_$i/$RUN.gain.root"
 
         if [[ ! -f "$CALIBDIR/Tel_$i/$RUN.gain.root" ]]; then
             echo "Processing gains from laser/flash run $RUN, telescope $i"
-            RUNFILE=`find -L $DDIR -name "$RUN.cvbf"`
+            RUNFILE=$(find -L "$DDIR" -name "$RUN.cvbf")
             if [[ -f $RUNFILE ]]; then
-                $EVNDISPSYS/scripts/VTS/SPANALYSIS.evndisp_laser_run.sh $i $RUNFILE
+                "$EVNDISPSYS"/scripts/VTS/SPANALYSIS.evndisp_laser_run.sh "$i" "$RUNFILE"
             else
                 echo "Missing laser/flasher file $RUNFILE, please download it"
             fi
diff --git a/scripts/SPANALYSIS.evndisp_pedestal_events.sh b/scripts/SPANALYSIS.evndisp_pedestal_events.sh
index 9e76be3..db3031c 100755
--- a/scripts/SPANALYSIS.evndisp_pedestal_events.sh
+++ b/scripts/SPANALYSIS.evndisp_pedestal_events.sh
@@ -26,38 +26,48 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 RUNNUM=$1
 [[ "$2" ]] && SAMPLES=$2 || SAMPLES="0"
 [[ "$3" ]] && CALIBDIR=$3 || CALIBDIR="$VERITAS_USER_DATA_DIR/"
 
-OPT=" -calibrationsumwindow=20 -calibrationdirectory $CALIBDIR "
+OPT=(
+    -calibrationsumwindow=20
+    -calibrationdirectory
+    "$CALIBDIR"
+)
 
 #high gain mode
 if [[ $SAMPLES == "0" ]]; then
-	OPT="$OPT -runmode=1 -calibrationsumfirst=0 "
+    OPT+=(
+        -runmode=1
+        -calibrationsumfirst=0
+    )
 
 #low gain mode
 else
-	OPT="$OPT -runmode=6 -reconstructionparameter EVNDISP.reconstruction.LGCalibration.runparameter "
-
-	if [[ $SAMPLES == "64" ]]; then
-		OPT="$OPT -calibrationsumfirst=40 "
-	elif  [[ $SAMPLES == "128" ]]; then
-		OPT="$OPT -calibrationsumfirst=100 "
-	elif [[ $SAMPLES == "100" ]]; then
-		OPT="$OPT -calibrationsumfirst=75 "
-	else
-		echo "Invalid number of samples given, please fix the script."
-		exit 1
-	fi
+    OPT+=(
+        -runmode=6
+        -reconstructionparameter
+        EVNDISP.reconstruction.LGCalibration.runparameter
+    )
+
+    if [[ $SAMPLES == "64" ]]; then
+        OPT+=("-calibrationsumfirst=40")
+    elif  [[ $SAMPLES == "128" ]]; then
+        OPT+=("-calibrationsumfirst=100")
+    elif [[ $SAMPLES == "100" ]]; then
+        OPT+=("-calibrationsumfirst=75")
+    else
+        echo "Invalid number of samples given, please fix the script."
+        exit 1
+    fi
 fi
 
 # Run evndisp
-echo "$EVNDISPSYS/bin/evndisp -runnumber=$RUNNUM $OPT "
-$EVNDISPSYS/bin/evndisp -runnumber=$RUNNUM $OPT
+echo "$EVNDISPSYS/bin/evndisp -runnumber=$RUNNUM ${OPT[*]}"
+"$EVNDISPSYS"/bin/evndisp -runnumber="$RUNNUM" "${OPT[@]}"
 
 exit
diff --git a/scripts/SPANALYSIS.evndisp_tzeros.sh b/scripts/SPANALYSIS.evndisp_tzeros.sh
index e87ad31..cb97111 100755
--- a/scripts/SPANALYSIS.evndisp_tzeros.sh
+++ b/scripts/SPANALYSIS.evndisp_tzeros.sh
@@ -28,8 +28,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 RUNNUM=$1
@@ -40,24 +39,24 @@ fi
 [[ "$3" ]] && CALDB=$3   || CALDB="1"
 
 # Check if source vbf file exists
-SF=`find -L $VERITAS_DATA_DIR/data -name "$RUNNUM.cvbf"`
+SF=$(find -L "$VERITAS_DATA_DIR"/data -name "$RUNNUM.cvbf")
 if [[ ${#SF} = 0 ]]; then
     echo "ERROR: VERITAS source file $RUNNUM.cvbf not found in $VERITAS_DATA_DIR/data/"
     exit 1
 fi
 
 if [[ $CALDB == "1" ]]; then
-    OPT="$OPT -readCalibDB"
+    OPT=(-readCalibDB)
 else
-    OPT="$OPT -nocalibnoproblem"
+    OPT=(-nocalibnoproblem)
 fi
-echo $OPT
+echo "${OPT[*]}"
 
 # run options
-OPT="-runmode=7 -runnumber=$RUNNUM -teltoana=$TELTOANA $OPT"
+OPT=("-runmode=7" "-runnumber=$RUNNUM" "-teltoana=$TELTOANA" "${OPT[@]}")
 
 # Run evndisp
-echo "$EVNDISPSYS/bin/evndisp $OPT"
-$EVNDISPSYS/bin/evndisp $OPT
+echo "$EVNDISPSYS/bin/evndisp ${OPT[*]}"
+"$EVNDISPSYS"/bin/evndisp "${OPT[@]}"
 
 exit
diff --git a/scripts/SPANALYSIS.lowgainped.sh b/scripts/SPANALYSIS.lowgainped.sh
index 979d993..187d76c 100755
--- a/scripts/SPANALYSIS.lowgainped.sh
+++ b/scripts/SPANALYSIS.lowgainped.sh
@@ -2,7 +2,7 @@
 # script to run eventdisplay analysis for VTS data
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:59:00; h_vmem=2000M; tmpdir_size=25G
 
 if [ ! -n "$1" ] || [ ! -n "$2" ] || [ "$1" = "-h" ]; then
@@ -37,11 +37,7 @@ exit
 fi
 
 # Run init script
-bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
-
-# EventDisplay version
-EDVERSION=`$EVNDISPSYS/bin/evndisp --version | tr -d .`
+bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # create extra stdout for duplication of command output
 # look for ">&5" below
@@ -51,8 +47,8 @@ exec 5>&1
 RLIST=$1
 SUMSTART=$2
 [[ "$3" ]] && ODIR=$3 || ODIR="$VERITAS_EVNDISP_AUX_DIR"
-mkdir -p $ODIR
-[[ "$4" ]] && SUMWINDOW=$4   || SUMWINNDOW=20
+mkdir -p "$ODIR"
+[[ "$4" ]] && SUMWINDOW=$4 || SUMWINDOW=20
 [[ "$5" ]] && TELTOANA=$5 || TELTOANA=1234
 [[ "$6" ]] && NEVENTS=$6 || NEVENTS=-1
 
@@ -61,18 +57,18 @@ if [ ! -f "$RLIST" ] ; then
     echo "Error, runlist $RLIST not found, exiting..."
     exit 1
 fi
-FILES=`cat $RLIST`
+FILES=$(cat "$RLIST")
 
 # Output directory for error/output
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/$DATE/EVNDISP.LGAINPED"
-mkdir -p $LOGDIR
+mkdir -p "$LOGDIR"
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/SPANALYSIS.lowgainped_sub"
 
 
-NRUNS=`cat $RLIST | wc -l `
+NRUNS=$(cat "$RLIST" | wc -l )
 echo "total number of runs to analyze: $NRUNS"
 echo
 
@@ -89,10 +85,10 @@ do
 	-e "s|NNNN|$NEVENTS|" 		    \
 	-e  "s|CALIBFIRST|$SUMSTART|" 	    \
 	-e  "s|CALIBSUMWINDOW|$SUMWINDOW|"  \
-	$SUBSCRIPT.sh > $FSCRIPT.sh
+	"$SUBSCRIPT".sh > "$FSCRIPT".sh
 
-    chmod u+x $FSCRIPT.sh
-    echo $FSCRIPT.sh
+    chmod u+x "$FSCRIPT".sh
+    echo "$FSCRIPT".sh
 	# output selected input during submission:
 	echo "calibrationsumwindow $SUMWINDOW, start at $SUMSTART, $NEVENTS events "
 	echo "Output: $ODIR"
@@ -105,14 +101,15 @@ do
 
     # run locally or on cluster
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     if [[ $SUBC == *"ERROR"* ]]; then
-        echo $SUBC
+        echo "$SUBC"
         exit
     fi
-    echo $SUBC
+    echo "$SUBC"
     if [[ $SUBC == *qsub* ]]; then
-        JOBID=`$SUBC $FSCRIPT.sh`
+        # shellcheck disable=SC2086
+        JOBID=$($SUBC "$FSCRIPT".sh)
         # account for -terse changing the job number format
         if [[ $SUBC != *-terse* ]] ; then
             echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
@@ -127,18 +124,20 @@ do
         fi
     elif [[ $SUBC == *condor* ]]; then
         "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-        condor_submit $FSCRIPT.sh.condor
+        condor_submit "$FSCRIPT".sh.condor
     elif [[ $SUBC == *sbatch* ]]; then
-        $SUBC $FSCRIPT.sh
+        # shellcheck disable=SC2086
+        $SUBC "$FSCRIPT".sh
     elif [[ $SUBC == *parallel* ]]; then
-        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.dat
+        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts.dat
         echo "RUN $AFILE OLOG $FSCRIPT.log"
     fi
 done
 
 # Execute all FSCRIPTs locally in parallel
 if [[ $SUBC == *parallel* ]]; then
-    cat $LOGDIR/runscripts.dat | $SUBC
+    # shellcheck disable=SC2086
+    cat "$LOGDIR"/runscripts.dat | $SUBC
 fi
 
 exit
diff --git a/scripts/SPANALYSIS.make_DST.sh b/scripts/SPANALYSIS.make_DST.sh
index cefc39a..40655c5 100755
--- a/scripts/SPANALYSIS.make_DST.sh
+++ b/scripts/SPANALYSIS.make_DST.sh
@@ -2,7 +2,7 @@
 # script to make DST files from a raw data file
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=11:29:00; h_vmem=4000M; tmpdir_size=40G
 
 if [[ $# -lt 2 ]]; then
@@ -40,8 +40,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 RLIST=$1
@@ -56,13 +55,13 @@ if [[ ! -f "$RLIST" ]]; then
     echo "Error, runlist $RLIST not found, exiting..."
     exit 1
 fi
-RUNNUMS=`cat $RLIST`
+RUNNUMS=$(cat "$RLIST")
 
 # run scripts are written into this directory
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/$DATE/EVNDISP.ANADATA"
 echo -e "Log files will be written to:\n $LOGDIR"
-mkdir -p $LOGDIR
+mkdir -p "$LOGDIR"
 
 
 # check for the existence of a run parameter file corresponding
@@ -75,7 +74,7 @@ if [[ -z $RUNPFILE ]]; then
 	RUNPFILE="EVNDISP.reconstruction.LMULT.SW$SUMW.runparameter"
 
 	if [ ! -e "$RUNPDIR/$RUNPFILE" ]; then
-    		sed -e "s|XX|$SUMW|g" $RUNPDIR/EVNDISP.reconstruction.LMULT.SWXX.runparameter > $RUNPDIR/$RUNPFILE
+		sed -e "s|XX|$SUMW|g" "$RUNPDIR"/EVNDISP.reconstruction.LMULT.SWXX.runparameter > "$RUNPDIR"/"$RUNPFILE"
 	fi
 fi
 
@@ -94,32 +93,35 @@ for RUN in $RUNNUMS; do
         -e "s|LLLOWGAIN|$LMULT|" \
         -e "s|OUTPUTDIR|$ODIR|" \
         -e "s|RRRRPFILE|$RUNPFILE|" \
-        -e "s|SUMWINDOW|$SUMW|" $SUBSCRIPT.sh > $FSCRIPT.sh
+        -e "s|SUMWINDOW|$SUMW|" "$SUBSCRIPT".sh > "$FSCRIPT".sh
 
-    chmod u+x $FSCRIPT.sh
-    echo $FSCRIPT.sh
+    chmod u+x "$FSCRIPT".sh
+    echo "$FSCRIPT".sh
 
     # run locally or on cluster
     SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-    SUBC=`eval "echo \"$SUBC\""`
+    SUBC=$(eval "echo \"$SUBC\"")
     if [[ $SUBC == *qsub* ]]; then
-        JOBID=`$SUBC $FSCRIPT.sh`
+        # shellcheck disable=SC2086
+        JOBID=$($SUBC "$FSCRIPT".sh)
 		echo "RUN $RUN: JOBID $JOBID"
     elif [[ $SUBC == *condor* ]]; then
         "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-        condor_submit $FSCRIPT.sh.condor
+        condor_submit "$FSCRIPT".sh.condor
     elif [[ $SUBC == *sbatch* ]]; then
-            $SUBC $FSCRIPT.sh
+            # shellcheck disable=SC2086
+            $SUBC "$FSCRIPT".sh
     elif [[ $SUBC == *parallel* ]]; then
-        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.dat
+        echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts.dat
     elif [[ $SUBC == *simple* ]]; then
-        $FSCRIPT.sh |& tee $FSCRIPT.log
+        "$FSCRIPT".sh |& tee "$FSCRIPT".log
     fi
 done
 
 # Execute all FSCRIPTs locally in parallel
 if [[ $SUBC == *parallel* ]]; then
-    cat $LOGDIR/runscripts.dat | $SUBC
+    # shellcheck disable=SC2086
+    cat "$LOGDIR"/runscripts.dat | $SUBC
 fi
 
 exit
diff --git a/scripts/UTILITY.downloadSoundingDatafromUWYO.sh b/scripts/UTILITY.downloadSoundingDatafromUWYO.sh
index b727f91..899305d 100755
--- a/scripts/UTILITY.downloadSoundingDatafromUWYO.sh
+++ b/scripts/UTILITY.downloadSoundingDatafromUWYO.sh
@@ -26,21 +26,21 @@ MONTH=( 01 02 03 04 05 06 07 08 09 10 11 12 )
 DAY=(   31 28 31 30 31 30 31 31 30 31 30 30 )
 NMONTH=${#MONTH[@]}
 
-for (( y = $YEAR1; y <= $YEAR2; y++ ))
+for (( y = YEAR1; y <= YEAR2; y++ ))
 do
     echo "Fetching $y"
 
-    for (( i = 0 ; i < $NMONTH; i++ ))
+    for (( i = 0 ; i < NMONTH; i++ ))
     do
         M=${MONTH[$i]}
         D=${DAY[$i]}
         ONAME="sounding_${y}${M}"
-        echo $M   $D   $ONAME
+        echo "$M"   "$D"   "$ONAME"
 
-        wget --output-document=$ONAME.dat2 "http://weather.uwyo.edu/cgi-bin/sounding?region=naconf&TYPE=TEXT%3ALIST&YEAR=${y}&MONTH=${M}&FROM=0100&TO=${D}12&STNM=${USM}&REPLOT=1"
+        wget --output-document="$ONAME".dat2 "http://weather.uwyo.edu/cgi-bin/sounding?region=naconf&TYPE=TEXT%3ALIST&YEAR=${y}&MONTH=${M}&FROM=0100&TO=${D}12&STNM=${USM}&REPLOT=1"
 
-        sed -e :a -e 's/<[^>]*>//g;/</N;//ba' $ONAME.dat2 > $ONAME.dat
-        rm -f $ONAME.dat2
+        sed -e :a -e 's/<[^>]*>//g;/</N;//ba' "$ONAME".dat2 > "$ONAME".dat
+        rm -f "$ONAME".dat2
 
     done
 done
diff --git a/scripts/UTILITY.sortRunsInSubDirectories.sh b/scripts/UTILITY.sortRunsInSubDirectories.sh
index ba39f60..a680bbf 100755
--- a/scripts/UTILITY.sortRunsInSubDirectories.sh
+++ b/scripts/UTILITY.sortRunsInSubDirectories.sh
@@ -30,16 +30,16 @@ getNumberedDirectory()
     else
         ODIR="${TDIR}/${TRUN:0:2}/"
     fi
-    mkdir -p ${ODIR}
-    echo ${ODIR}
+    mkdir -p "${ODIR}"
+    echo "${ODIR}"
 }
 
 FLIST=$(find "${DDIR}" -name "[0-9]*.*${SUFF}")
 
 for F in ${FLIST}
 do
-    RUNN=$(basename ${F})
+    RUNN=$(basename "${F}")
     RUNN="${RUNN%%.*}"
-    ODIR=$(getNumberedDirectory $RUNN)
-    mv -f -v ${F} ${ODIR}
+    ODIR=$(getNumberedDirectory "$RUNN")
+    mv -f -v "${F}" "${ODIR}"
 done
diff --git a/scripts/db_scripts/db_FADCsettings.sh b/scripts/db_scripts/db_FADCsettings.sh
index 10061a5..d4d5ce7 100755
--- a/scripts/db_scripts/db_FADCsettings.sh
+++ b/scripts/db_scripts/db_FADCsettings.sh
@@ -18,4 +18,4 @@ TELID="$3"
 
 QUERY="select c.pixel_id , s.fadc_id, c.fadc_channel from tblFADC_Slot_Relation as s, tblFADC_Channel_Relation as c where s.db_start_time < \"${STARTDATE}\" and c.db_start_time < \"${STARTDATE}\" and ( s.db_end_time IS NULL or s.db_end_time > \"${ENDDATE}\" ) and ( c.db_end_time IS NULL or c.db_end_time > \"${ENDDATE}\" ) and s.fadc_crate=c.fadc_crate and s.fadc_slot=c.fadc_slot and s.telescope_id=c.telescope_id and c.pixel_id IS NOT NULL and s.telescope_id=${TELID} order by c.pixel_id ;"
 
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_HVsettings.sh b/scripts/db_scripts/db_HVsettings.sh
index 51e47eb..fb33c76 100755
--- a/scripts/db_scripts/db_HVsettings.sh
+++ b/scripts/db_scripts/db_HVsettings.sh
@@ -18,4 +18,4 @@ TELID="$3"
 
 QUERY="select * FROM tblHV_Telescope${TELID}_Status WHERE channel > 0 AND (db_start_time >=\"${STARTDATE}\" - INTERVAL 1 MINUTE) AND (db_start_time <= \"${ENDDATE}\" );"
 
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_L1_TriggerInfo.sh b/scripts/db_scripts/db_L1_TriggerInfo.sh
index 82c74b9..5492e07 100755
--- a/scripts/db_scripts/db_L1_TriggerInfo.sh
+++ b/scripts/db_scripts/db_L1_TriggerInfo.sh
@@ -17,4 +17,4 @@ fi
 RUN=$1
 QUERY="select timestamp, telescope_id, pixel_id, rate from tblL1_TriggerInfo, tblRun_Info where timestamp >= tblRun_Info.data_start_time - INTERVAL 1 MINUTE AND timestamp <=  tblRun_Info.data_end_time + INTERVAL 1 MINUTE AND tblRun_Info.run_id=${RUN};"
 
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_L3.sh b/scripts/db_scripts/db_L3.sh
index a30cf25..dc95145 100755
--- a/scripts/db_scripts/db_L3.sh
+++ b/scripts/db_scripts/db_L3.sh
@@ -27,5 +27,5 @@ if [[ "${STARTDATE}" == *NULL* ]] || [[ "${ENDDATE}" == *NULL* ]]; then
     echo ""
 else
     QUERY="SELECT timestamp, run_id, L3, L3orVDAQBusy, VDAQBusy, SpareBusy, PED, OC, VDAQBusyScaler, L3orVDAQBusyScaler, TenMHzScaler FROM tblL3_Array_TriggerInfo WHERE timestamp >= ${TIMESTART} AND timestamp <= ${TIMEEND};"
-    $($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
+    $("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
 fi
diff --git a/scripts/db_scripts/db_VPM.sh b/scripts/db_scripts/db_VPM.sh
index e645532..3288d13 100755
--- a/scripts/db_scripts/db_VPM.sh
+++ b/scripts/db_scripts/db_VPM.sh
@@ -15,12 +15,12 @@ STARTDATE="$1"
 ENDDATE="$2"
 TELID="$3"
 
-STARTMJD=$($EVNDISPSYS/bin/printMJD "${STARTDATE}")
-ENDMJD=$($EVNDISPSYS/bin/printMJD "${ENDDATE}")
+STARTMJD=$("$EVNDISPSYS"/bin/printMJD "${STARTDATE}")
+ENDMJD=$("$EVNDISPSYS"/bin/printMJD "${ENDDATE}")
 
 if [[ "${STARTDATE}" == *NULL* ]] || [[ "${ENDDATE}" == *NULL* ]]; then
     echo ""
 else
     QUERY="SELECT mjd,ra,decl FROM tblPointing_Monitor_Telescope${TELID}_Calibrated_Pointing WHERE mjd<=${ENDMJD} AND mjd>=${STARTMJD}"
-    $($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}"  | sed 's/\t/|/g'
+    $("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}"  | sed 's/\t/|/g'
 fi
diff --git a/scripts/db_scripts/db_camerarotation.sh b/scripts/db_scripts/db_camerarotation.sh
index e0fc04c..273b10a 100755
--- a/scripts/db_scripts/db_camerarotation.sh
+++ b/scripts/db_scripts/db_camerarotation.sh
@@ -17,4 +17,4 @@ fi
 STARTDATE="$1"
 ENDDATE="$2"
 QUERY="select telescope_id, version, pmt_rotation from tblPointing_Monitor_Camera_Parameters where start_date <=\"${STARTDATE}\" and end_date >\"${ENDDATE}\" ORDER BY version DESC"
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}"  | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}"  | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_copy_old_laser_calibration.sh b/scripts/db_scripts/db_copy_old_laser_calibration.sh
index ea4f83d..ef98a5a 100755
--- a/scripts/db_scripts/db_copy_old_laser_calibration.sh
+++ b/scripts/db_scripts/db_copy_old_laser_calibration.sh
@@ -34,31 +34,31 @@ fill_gain_or_toff()
 {
     LRUN=${1}
     if [[ -e ${CALIBDIR}/Tel_${2}/${LRUN}.${3/set/} ]]; then
-        cp -v ${CALIBDIR}/Tel_${2}/${LRUN}.${3/set/} ${LRUN}/${LRUN}.${3}_TEL${2}
-        sed -i "1s/^/channel_id|${3}_mean|${3}_var\n/" ${LRUN}/${LRUN}.${3}_TEL${2}
-        sed -i "s/ /|/g" ${LRUN}/${LRUN}.${3}_TEL${2}
+        cp -v "${CALIBDIR}"/Tel_"${2}"/"${LRUN}"."${3/set/}" "${LRUN}"/"${LRUN}"."${3}"_TEL"${2}"
+        sed -i "1s/^/channel_id|${3}_mean|${3}_var\n/" "${LRUN}"/"${LRUN}"."${3}"_TEL"${2}"
+        sed -i "s/ /|/g" "${LRUN}"/"${LRUN}"."${3}"_TEL"${2}"
     else
         echo "No calibration found for ${LRUN} ${2}"
         echo "${CALIBDIR}/Tel_${2}/${LRUN}.${3}"
     fi
 }
 
-DBTEXTFILE=$(get_db_text_tar_file ${1})
+DBTEXTFILE=$(get_db_text_tar_file "${1}")
 if [[ ! -e ${DBTEXTFILE} ]]; then
     echo "Error: db tar file not found: ${DBTEXTFILE}"
     exit
 fi
 mkdir -p tmp_update_laser_run
 cd tmp_update_laser_run || exit
-cp -v ${DBTEXTFILE} .
-tar -xzf ${DBTEXTFILE}
+cp -v "${DBTEXTFILE}" .
+tar -xzf "${DBTEXTFILE}"
 
 for T in 1 2 3 4
 do
     for C in gain toffset
     do
 #        if [[ ! -e ${LRUN}/${LASERRUN}.${C}_TEL${T} ]]; then
-            fill_gain_or_toff $LASERRUN ${T} $C
+            fill_gain_or_toff "$LASERRUN" ${T} $C
 #        else
 #            echo "Calibration files $C exists for run $LASERRUN"
 #        fi
diff --git a/scripts/db_scripts/db_fir.sh b/scripts/db_scripts/db_fir.sh
index 9ea3cf0..93fd8dc 100755
--- a/scripts/db_scripts/db_fir.sh
+++ b/scripts/db_scripts/db_fir.sh
@@ -15,4 +15,4 @@ STARTDATE="$1"
 ENDDATE="$2"
 
 QUERY="SELECT timestamp, telescope_id, ambient_temp, radiant_sky_temp FROM tblFIR_Pyrometer_Info  WHERE timestamp >= \"${STARTDATE}\" AND timestamp < \"${ENDDATE}\""
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_gain.sh b/scripts/db_scripts/db_gain.sh
index a00128a..8d23a20 100755
--- a/scripts/db_scripts/db_gain.sh
+++ b/scripts/db_scripts/db_gain.sh
@@ -18,4 +18,4 @@ LOWGAIN="0"
 
 QUERY="SELECT * FROM(SELECT tbl.channel_id, tbl.gain_mean, tbl.gain_var FROM tblEventDisplay_Analysis_Calibration_Flasher AS tbl WHERE tbl.telescope = ${TELID} AND  tbl.run_id = ${RUN} AND tbl.high_low_gain_flag = $LOWGAIN ORDER BY tbl.update_time DESC ) AS BIG_table GROUP BY channel_id;"
 
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}" | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}" | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_laserrun.sh b/scripts/db_scripts/db_laserrun.sh
index e4a2789..6d3418d 100755
--- a/scripts/db_scripts/db_laserrun.sh
+++ b/scripts/db_scripts/db_laserrun.sh
@@ -1,5 +1,4 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 #
 
 if [ ! -n "$1" ] || [ "$1" = "-h" ]; then
@@ -16,6 +15,6 @@ exit
 fi
 
 RUN=$1
-QUERY="SELECT info.run_id, grp_cmt.excluded_telescopes, info.config_mask FROM tblRun_Info AS info, tblRun_Group AS grp, tblRun_GroupComment AS grp_cmt, (SELECT group_id FROM tblRun_Group WHERE run_id=$1) AS run_grp WHERE grp_cmt.group_id = run_grp.group_id AND grp_cmt.group_type='laser' AND grp_cmt.group_id=grp.group_id AND grp.run_id=info.run_id AND (info.run_type='flasher' OR info.run_type='laser');"
+QUERY="SELECT info.run_id, grp_cmt.excluded_telescopes, info.config_mask FROM tblRun_Info AS info, tblRun_Group AS grp, tblRun_GroupComment AS grp_cmt, (SELECT group_id FROM tblRun_Group WHERE run_id=$RUN) AS run_grp WHERE grp_cmt.group_id = run_grp.group_id AND grp_cmt.group_type='laser' AND grp_cmt.group_id=grp.group_id AND grp.run_id=info.run_id AND (info.run_type='flasher' OR info.run_type='laser');"
 
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_lidar.sh b/scripts/db_scripts/db_lidar.sh
index f63c54f..5b17957 100755
--- a/scripts/db_scripts/db_lidar.sh
+++ b/scripts/db_scripts/db_lidar.sh
@@ -18,5 +18,5 @@ if [[ "${STARTDATE}" == *NULL* ]] || [[ "${ENDDATE}" == *NULL* ]]; then
     echo ""
 else
     QUERY="SELECT * FROM tblLIDAR_Info WHERE timestamp >= \"${STARTDATE}\" AND timestamp < \"${ENDDATE}\""
-    $($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
+    $("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
 fi
diff --git a/scripts/db_scripts/db_mysqldb.sh b/scripts/db_scripts/db_mysqldb.sh
index c4d7019..bca5cc6 100755
--- a/scripts/db_scripts/db_mysqldb.sh
+++ b/scripts/db_scripts/db_mysqldb.sh
@@ -13,7 +13,7 @@ fi
 
 # get url of veritas db
 PARAFILE="${VERITAS_EVNDISP_AUX_DIR}/ParameterFiles/EVNDISP.global.runparameter"
-MYSQLDB=`grep '^\*[ \t]*DBSERVER[ \t]*mysql://' ${PARAFILE} | egrep -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}'`
+MYSQLDB=$(grep '^\*[ \t]*DBSERVER[ \t]*mysql://' "${PARAFILE}" | grep -E -o '[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}\.[[:alpha:]]{1,20}')
 if [ ! -n "$MYSQLDB" ] ; then
     echo "Error: DBSERVER parameters not found in ${PARAFILE}"
     exit 1
diff --git a/scripts/db_scripts/db_pack_new_directories.sh b/scripts/db_scripts/db_pack_new_directories.sh
index fa8a33e..3643b6c 100755
--- a/scripts/db_scripts/db_pack_new_directories.sh
+++ b/scripts/db_scripts/db_pack_new_directories.sh
@@ -15,17 +15,17 @@ get_run_directory()
     fi
     echo "${DBTEXTDIR}/${SRUN}"
 }
-LDIR=$(find ${DBTEXTDIR} -type d -name "[0-9][0-9][0-9]*")
+LDIR=$(find "${DBTEXTDIR}" -type d -name "[0-9][0-9][0-9]*")
 
 PDIR=$(pwd)
 
 for L in ${LDIR}
 do
-    RUN=$(basename $L)
-    TDIR=$(get_run_directory $RUN)
-    echo $RUN $TDIR/$RUN
+    RUN=$(basename "$L")
+    TDIR=$(get_run_directory "$RUN")
+    echo "$RUN" "$TDIR"/"$RUN"
     cd "$TDIR" || exit
-    tar -czf ${RUN}.tar.gz ${RUN}
+    tar -czf "${RUN}".tar.gz "${RUN}"
 done
 
 cd "${PDIR}" || exit
diff --git a/scripts/db_scripts/db_rawpointing.sh b/scripts/db_scripts/db_rawpointing.sh
index d92209f..8f9fcbe 100755
--- a/scripts/db_scripts/db_rawpointing.sh
+++ b/scripts/db_scripts/db_rawpointing.sh
@@ -28,5 +28,5 @@ if [[ "${STARTDATE}" == *NULL* ]] || [[ "${TIMEEND}" == *NULL* ]]; then
     echo ""
 else
     QUERY="SELECT timestamp, elevation_raw, azimuth_raw, elevation_meas, azimuth_meas, elevation_target, azimuth_target FROM tblPositioner_Telescope${TELID}_Status WHERE timestamp >= ${TIMESTART} AND timestamp <= ${TIMEEND};"
-    $($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
+    $("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
 fi
diff --git a/scripts/db_scripts/db_run.sh b/scripts/db_scripts/db_run.sh
index c65ad60..ab15b02 100755
--- a/scripts/db_scripts/db_run.sh
+++ b/scripts/db_scripts/db_run.sh
@@ -28,7 +28,7 @@ OVERWRITE="0"
 NTEL="4"
 
 DBDIR="${VERITAS_DATA_DIR%/}/shared/DBTEXT/"
-mkdir -p ${DBDIR}
+mkdir -p "${DBDIR}"
 
 getDBTextFileDirectory()
 {
@@ -38,7 +38,7 @@ getDBTextFileDirectory()
     else
         ODIR="${DBDIR%/}/${TRUN:0:2}/${TRUN}"
     fi
-    echo ${ODIR}
+    echo "${ODIR}"
 }
 
 get_file_status()
@@ -51,10 +51,10 @@ get_file_status()
     elif [[ -e ${TFIL} ]]; then
         echo "2"
     else
-        TARF="$(getDBTextFileDirectory ${RRUN}).tar.gz"
+        TARF="$(getDBTextFileDirectory "${RRUN}").tar.gz"
         if [[ -e ${TARF} ]]; then
-            FFIL="${RRUN}/$(basename ${TFIL})"
-            CFIL=$(tar -tzf ${TARF} ${FFIL} 2>/dev/null)
+            FFIL="${RRUN}/$(basename "${TFIL}")"
+            CFIL=$(tar -tzf "${TARF}" "${FFIL}" 2>/dev/null)
             if [[ "${CFIL}" == "${FFIL}" ]]; then
                 echo "1"
             else
@@ -68,7 +68,7 @@ get_file_status()
 
 get_start_time()
 {
-    OFIL="$(getDBTextFileDirectory ${RUN})/${RUN}.runinfo"
+    OFIL="$(getDBTextFileDirectory "${RUN}")/${RUN}.runinfo"
     if [[ "${1:-}" == "DB" ]]; then
         field_name="db_start_time"
     else
@@ -86,13 +86,13 @@ get_start_time()
             done
         fi
         start_time="${a[$start_time_index]}"
-    done < ${OFIL}
+    done < "${OFIL}"
     echo "${start_time}"
 }
 
 get_end_time()
 {
-    OFIL="$(getDBTextFileDirectory ${RUN})/${RUN}.runinfo"
+    OFIL="$(getDBTextFileDirectory "${RUN}")/${RUN}.runinfo"
     if [[ "${1:-}" == "DB" ]]; then
         field_name="db_end_time"
     else
@@ -110,7 +110,7 @@ get_end_time()
             done
         fi
         end_time="${a[$end_time_index]}"
-    done < ${OFIL}
+    done < "${OFIL}"
     # add 1 minute to end time to be save
     end_time=$(date -d "${end_time} 1 minutes" +'%Y-%m-%d %H:%M:%S')
     echo "${end_time}"
@@ -118,19 +118,19 @@ get_end_time()
 
 get_laser_run()
 {
-    OFIL="$(getDBTextFileDirectory ${RUN})/${RUN}.laserrun"
+    OFIL="$(getDBTextFileDirectory "${RUN}")/${RUN}.laserrun"
     LASERRUN=""
     while IFS="|" read -ra a; do
         if [[ ${a[0]} != "run_id" ]]; then
             LASERRUN="${LASERRUN} ${a[0]}"
         fi
-    done < ${OFIL}
-    echo ${LASERRUN}
+    done < "${OFIL}"
+    echo "${LASERRUN}"
 }
 
 get_excluded_telescopes()
 {
-    OFIL="$(getDBTextFileDirectory ${RUN})/${RUN}.laserrun"
+    OFIL="$(getDBTextFileDirectory "${RUN}")/${RUN}.laserrun"
     excluded_telescopes=""
     while IFS="|" read -ra a; do
         if [[ ${a[0]} == "run_id" ]]; then
@@ -145,8 +145,8 @@ get_excluded_telescopes()
         if [[ ${a[0]} == "$1" ]]; then
             excluded_telescopes=${a[$excluded_telescopes_index]}
         fi
-    done < ${OFIL}
-    echo ${excluded_telescopes}
+    done < "${OFIL}"
+    echo "${excluded_telescopes}"
 }
 
 
@@ -166,13 +166,13 @@ hasbitset()
 
 get_source_id()
 {
-    OFIL="$(getDBTextFileDirectory ${RUN})/${RUN}.runinfo"
+    OFIL="$(getDBTextFileDirectory "${RUN}")/${RUN}.runinfo"
     local tar_file
     tar_file="$(getDBTextFileDirectory "${RUN}").tar.gz"
     if [[ ! -e ${OFIL} ]] && [[ -e ${tar_file} ]]; then
         OFIL=$(tar -xzf "$tar_file" "${RUN}/${RUN}.runinfo" -O)
     else
-        OFIL=$(cat $OFIL)
+        OFIL=$(cat "$OFIL")
     fi
     source_index=0
     while IFS="|" read -ra a; do
@@ -187,7 +187,7 @@ get_source_id()
         fi
         source_id="${a[$source_index]}"
     done <<< "$OFIL"
-    echo ${source_id}
+    echo "${source_id}"
 }
 
 # generic function to read call scripts reading from DB
@@ -199,20 +199,20 @@ read_run_from_DB()
     [[ "$3" ]] && TELID=$3 || TELID=""
     [[ "$4" ]] && USETIME=$4 || USETIME="0"
     if [[ -z ${TELID} ]]; then
-        OFIL="$(getDBTextFileDirectory ${RRUN})/${RRUN}.${TTOOL}"
+        OFIL="$(getDBTextFileDirectory "${RRUN}")/${RRUN}.${TTOOL}"
     else
-        OFIL="$(getDBTextFileDirectory ${RRUN})/${RRUN}.${TTOOL}_TEL${TELID}"
+        OFIL="$(getDBTextFileDirectory "${RRUN}")/${RRUN}.${TTOOL}_TEL${TELID}"
     fi
-    FILESTATUS="$(get_file_status ${RRUN} ${OFIL})"
+    FILESTATUS="$(get_file_status "${RRUN}" "${OFIL}")"
     if [[ ${FILESTATUS} == 0 ]]; then
-        mkdir -p "$(getDBTextFileDirectory ${RRUN})"
-        rm -f ${OFIL}
+        mkdir -p "$(getDBTextFileDirectory "${RRUN}")"
+        rm -f "${OFIL}"
         if [[ $USETIME -eq "0" ]]; then
             cmd="./db_${TTOOL}.sh ${RRUN} ${TELID}"
         else
             cmd="./db_${TTOOL}.sh \"$(get_start_time "")\" \"$(get_end_time "")\" ${TELID}"
         fi
-        eval "$cmd" > ${OFIL}
+        eval "$cmd" > "${OFIL}"
         echo "${TTOOL} file (written): ${OFIL}"
     elif [[ ${FILESTATUS} == 1 ]]; then
         echo "${TTOOL} file (in tar package): ${OFIL}"
@@ -228,18 +228,18 @@ read_laser_run_and_dqm()
     for L in "${LASERRUN[@]}"
     do
         if [[ -n ${L} ]]; then
-            read_run_from_DB rundqm ${L}
+            read_run_from_DB rundqm "${L}"
         fi
     done
 }
 
 read_target()
 {
-    OFIL="$(getDBTextFileDirectory ${RUN})/${RUN}.target"
+    OFIL="$(getDBTextFileDirectory "${RUN}")/${RUN}.target"
     source_id=$(get_source_id)
-    FILESTATUS="$(get_file_status ${RUN} ${OFIL})"
+    FILESTATUS="$(get_file_status "${RUN}" "${OFIL}")"
     if [[ ${FILESTATUS} == 0 ]]; then
-        ./db_target.sh "${source_id}" > ${OFIL}
+        ./db_target.sh "${source_id}" > "${OFIL}"
         echo "target file (written): ${OFIL}"
     elif [[ ${FILESTATUS} == 1 ]]; then
         echo "target file (in tar package): ${OFIL}"
@@ -250,18 +250,18 @@ read_target()
 
 read_camera_rotation()
 {
-    OFIL="$(getDBTextFileDirectory ${RUN})/${RUN}.camerarotation"
-    read_run_from_DB camerarotation ${RUN} "" 1
+    OFIL="$(getDBTextFileDirectory "${RUN}")/${RUN}.camerarotation"
+    read_run_from_DB camerarotation "${RUN}" "" 1
 }
 
 read_pixel_data()
 {
     read_run_from_DB L1_TriggerInfo
 
-    for (( j=0; j<${NTEL}; j++ ));
+    for (( j=0; j<NTEL; j++ ));
     do
-        read_run_from_DB FADCsettings ${RUN} $j 1
-        read_run_from_DB HVsettings ${RUN} $j 1
+        read_run_from_DB FADCsettings "${RUN}" $j 1
+        read_run_from_DB HVsettings "${RUN}" $j 1
     done
 }
 
@@ -270,34 +270,34 @@ read_laser_calibration()
     mapfile -t LASERRUN < <(get_laser_run)
     for L in "${LASERRUN[@]}"
     do
-        excluded_telescopes=$(get_excluded_telescopes ${L})
-        for (( j=1; j<=${NTEL}; j++ ));
+        excluded_telescopes=$(get_excluded_telescopes "${L}")
+        for (( j=1; j<=NTEL; j++ ));
         do
-            bittest=$(hasbitset $excluded_telescopes $j)
+            bittest=$(hasbitset "$excluded_telescopes" $j)
             if [[ $bittest == "1" ]] && [[ $excluded_telescopes != "0" ]]; then
                 continue
             fi
-            read_run_from_DB gain ${L} ${j}
-            read_run_from_DB toffset ${L} ${j}
+            read_run_from_DB gain "${L}" ${j}
+            read_run_from_DB toffset "${L}" ${j}
         done
     done
 }
 
 read_pointing()
 {
-    for (( j=0; j<${NTEL}; j++ ));
+    for (( j=0; j<NTEL; j++ ));
     do
-        read_run_from_DB VPM ${RUN} $j 1
-        read_run_from_DB rawpointing ${RUN} $j 1
+        read_run_from_DB VPM "${RUN}" $j 1
+        read_run_from_DB rawpointing "${RUN}" $j 1
     done
 }
 
 read_run_from_DB runinfo
 read_run_from_DB rundqm
 # Re-read laser data if tarball is missing OR if sidecar .laserrun file is absent
-RUND="$(getDBTextFileDirectory ${RUN})"
+RUND="$(getDBTextFileDirectory "${RUN}")"
 if [[ ! -e "${RUND}.tar.gz" ]] || \
-   [[ $(get_file_status ${RUN} "${RUND}/${RUN}.laserrun") == "0" ]] || \
+   [[ $(get_file_status "${RUN}" "${RUND}/${RUN}.laserrun") == "0" ]] || \
    [[ ${OVERWRITE} == "1" ]]; then
     read_laser_run_and_dqm
     read_laser_calibration
@@ -306,7 +306,7 @@ read_target
 read_camera_rotation
 read_pixel_data
 read_pointing
-read_run_from_DB lidar ${RUN} "" 1
-read_run_from_DB L3 ${RUN} "" 1
-read_run_from_DB weather ${RUN} "" 1
-read_run_from_DB fir ${RUN} "" 1
+read_run_from_DB lidar "${RUN}" "" 1
+read_run_from_DB L3 "${RUN}" "" 1
+read_run_from_DB weather "${RUN}" "" 1
+read_run_from_DB fir "${RUN}" "" 1
diff --git a/scripts/db_scripts/db_rundqm.sh b/scripts/db_scripts/db_rundqm.sh
index 1f58a4c..adb1a59 100755
--- a/scripts/db_scripts/db_rundqm.sh
+++ b/scripts/db_scripts/db_rundqm.sh
@@ -25,4 +25,4 @@ RUNSTART=$1
 [[ "$2" ]] && RUNSTOPP=$2 || RUNSTOPP=$1
 QUERY="SELECT run_id , data_category   , status   , status_reason , tel_cut_mask , usable_duration , time_cut_mask , light_level , vpm_config_mask , authors  , comment from tblRun_Analysis_Comments where run_id>=${RUNSTART} and run_id<=${RUNSTOPP};"
 
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}" | sed 's/\t/|/g' | sed 's/\r//g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}" | sed 's/\t/|/g' | sed 's/\r//g'
diff --git a/scripts/db_scripts/db_runinfo.sh b/scripts/db_scripts/db_runinfo.sh
index e031c36..3589ecf 100755
--- a/scripts/db_scripts/db_runinfo.sh
+++ b/scripts/db_scripts/db_runinfo.sh
@@ -25,4 +25,4 @@ RUNSTART=$1
 [[ "$2" ]] && RUNSTOPP=$2 || RUNSTOPP=$1
 QUERY="select * from tblRun_Info where run_id>=${RUNSTART} and run_id<=${RUNSTOPP};"
 
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_target.sh b/scripts/db_scripts/db_target.sh
index ae441f1..1947e93 100755
--- a/scripts/db_scripts/db_target.sh
+++ b/scripts/db_scripts/db_target.sh
@@ -18,4 +18,4 @@ fi
 TARGET=$1
 QUERY="select * from tblObserving_Sources where source_id like convert( _utf8 '$TARGET' using latin1);"
 
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}" | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_toffset.sh b/scripts/db_scripts/db_toffset.sh
index 58e80df..9922154 100755
--- a/scripts/db_scripts/db_toffset.sh
+++ b/scripts/db_scripts/db_toffset.sh
@@ -18,4 +18,4 @@ LOWGAIN="0"
 
 QUERY="SELECT * FROM(SELECT tbl.channel_id, tbl.toffset_mean, tbl.toffset_var FROM tblEventDisplay_Analysis_Calibration_Flasher AS tbl WHERE tbl.telescope = ${TELID} AND  tbl.run_id = ${RUN} AND tbl.high_low_gain_flag = $LOWGAIN ORDER BY tbl.update_time DESC ) AS BIG_table GROUP BY channel_id;"
 
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}" | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VOFFLINE; ${QUERY}" | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_update_old_laser_files.sh b/scripts/db_scripts/db_update_old_laser_files.sh
index e7b492f..72e08b2 100755
--- a/scripts/db_scripts/db_update_old_laser_files.sh
+++ b/scripts/db_scripts/db_update_old_laser_files.sh
@@ -32,7 +32,7 @@ get_db_text_tar_file()
 
 get_date()
 {
-    RUNINFOSTRING=$(tar -axf ${2} ${1}/${1}.runinfo -O)
+    RUNINFOSTRING=$(tar -axf "${2}" "${1}"/"${1}".runinfo -O)
     DATE=$(echo "${RUNINFOSTRING}" | cut -d '|' -f 5 | grep -v db_start_time | tr -d '-')
     echo "${DATE:0:8}"
 
@@ -42,28 +42,28 @@ fill_laser_run()
 {
     mkdir -p tmp_update_laser_run
     cd tmp_update_laser_run || exit
-    cp ${2} .
-    TFILE=$(basename ${2})
-    tar -xzf ${TFILE}
-    rm -f ${TFILE}
+    cp "${2}" .
+    TFILE=$(basename "${2}")
+    tar -xzf "${TFILE}"
+    rm -f "${TFILE}"
     echo "Updating laser file ${1}/${1}.laserrun"
-    echo "run_id|excluded_telescopes|config_mask" >> ${1}/${1}.laserrun
-    echo "${3}|0|15" >> ${1}/${1}.laserrun
+    echo "run_id|excluded_telescopes|config_mask" >> "${1}"/"${1}".laserrun
+    echo "${3}|0|15" >> "${1}"/"${1}".laserrun
     cd .. || exit
 }
 
-DBTEXTFILE=$(get_db_text_tar_file ${1})
+DBTEXTFILE=$(get_db_text_tar_file "${1}")
 if [[ ! -e ${DBTEXTFILE} ]]; then
     echo "Error: db tar file nout found: ${DBTEXTFILE}"
     exit
 fi
 
 echo "checking for laser runs for run ${1}"
-LASERSTRING=$(tar -axf ${DBTEXTFILE} ${1}/${1}.laserrun -O)
+LASERSTRING=$(tar -axf "${DBTEXTFILE}" "${1}"/"${1}".laserrun -O)
 if [ -z "${LASERSTRING}" ]; then
-    OBSDATE=$(get_date ${1} ${DBTEXTFILE})
+    OBSDATE=$(get_date "${1}" "${DBTEXTFILE}")
     echo "   Observation date is: ${OBSDATE} found in  ${2}"
-    LASERRUN=$(grep ${OBSDATE} ${2})
+    LASERRUN=$(grep "${OBSDATE}" "${2}")
     if [ -n "${LASERRUN}" ]; then
         echo "   FOUND ${LASERRUN} ${OBSDATE}"
         fill_laser_run "${1}" "${DBTEXTFILE}" "$(echo "$LASERRUN" | cut -d ' ' -f 2)"
diff --git a/scripts/db_scripts/db_update_tar_balls.sh b/scripts/db_scripts/db_update_tar_balls.sh
index 17b5ecc..f1a336a 100755
--- a/scripts/db_scripts/db_update_tar_balls.sh
+++ b/scripts/db_scripts/db_update_tar_balls.sh
@@ -28,11 +28,11 @@ get_run_directory()
 }
 PDIR=$(pwd)
 
-FILES=$(cat $FLIST)
+FILES=$(cat "$FLIST")
 
 for RUN in $FILES
 do
-    SUBDIR=$(get_run_directory $RUN)
+    SUBDIR=$(get_run_directory "$RUN")
 
     ORG_FILE="${DBTEXTDIR}/${SUBDIR}/${RUN}.tar.gz"
     if [[ ! -e "${ORG_FILE}" ]]; then
@@ -47,11 +47,11 @@ do
 
     # copy and unpack tar ball
     cd "${NEWDIR}/${SUBDIR}/" || exit
-    cp ${ORG_FILE} .
-    tar -xvzf ${RUN}.tar.gz
-    rm -f ${RUN}.tar.gz
+    cp "${ORG_FILE}" .
+    tar -xvzf "${RUN}".tar.gz
+    rm -f "${RUN}".tar.gz
     # pack again with all files
-    tar -cvzf ${RUN}.tar.gz ${RUN}
+    tar -cvzf "${RUN}".tar.gz "${RUN}"
 
     cd "${PDIR}" || exit
 done
diff --git a/scripts/db_scripts/db_weather.sh b/scripts/db_scripts/db_weather.sh
index 103048c..6b78a78 100755
--- a/scripts/db_scripts/db_weather.sh
+++ b/scripts/db_scripts/db_weather.sh
@@ -15,4 +15,4 @@ STARTDATE="$1"
 ENDDATE="$2"
 
 QUERY="SELECT timestamp, WS_mph_Avg, WS_mph_Max, WS_mph_Min, WindDir, AirTF_Avg, RH, Rain_in_Tot, SlrW_Avg, SlrkJ_Tot, BP_mbar_Avg FROM tblWeather_Status WHERE timestamp >= \"${STARTDATE}\" AND timestamp < \"${ENDDATE}\""
-$($EVNDISPSCRIPTS/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
+$("$EVNDISPSCRIPTS"/db_scripts/db_mysqldb.sh) -e "USE VERITAS; ${QUERY}"  | sed 's/\t/|/g'
diff --git a/scripts/db_scripts/db_write_fits_from_runlist.sh b/scripts/db_scripts/db_write_fits_from_runlist.sh
index 2f6d47c..20c4eb3 100755
--- a/scripts/db_scripts/db_write_fits_from_runlist.sh
+++ b/scripts/db_scripts/db_write_fits_from_runlist.sh
@@ -12,11 +12,11 @@ db_write_fits_from_runlist.sh: write DB FITS files from run list
 exit
 fi
 
-RUNS=$(cat $1)
+RUNS=$(cat "$1")
 IDIR="$VERITAS_DATA_DIR/shared/DBTEXT/"
 ODIR="./"
 
 for R in $RUNS
 do
-    python ./db_write_fits.py --run ${R} --input_path ${IDIR} --output_path ${ODIR}
+    python ./db_write_fits.py --run "${R}" --input_path "${IDIR}" --output_path ${ODIR}
 done
diff --git a/scripts/db_scripts/query_run_list.sh b/scripts/db_scripts/query_run_list.sh
index b8b8665..4a7cf69 100755
--- a/scripts/db_scripts/query_run_list.sh
+++ b/scripts/db_scripts/query_run_list.sh
@@ -13,10 +13,10 @@ query_run_list.sh: query DB and write DBTEXT files
 exit
 fi
 
-RUNS=$(cat $1)
+RUNS=$(cat "$1")
 [[ "$2" ]] && OVERW=$2 || OVERW="0"
 
 for R in $RUNS
 do
-    ./db_run.sh ${R} ${OVERW}
+    ./db_run.sh "${R}" "${OVERW}"
 done
diff --git a/scripts/helper_scripts/ANALYSIS.anasum_combine_sub.sh b/scripts/helper_scripts/ANALYSIS.anasum_combine_sub.sh
index 8d16cfc..c7270ec 100755
--- a/scripts/helper_scripts/ANALYSIS.anasum_combine_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.anasum_combine_sub.sh
@@ -2,8 +2,9 @@
 # script to combine anasum runs
 #
 # set observatory environmental variables
+# shellcheck source=/dev/null
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
-    source $EVNDISPSYS/setObservatory.sh VTS
+    source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
 
 # parameters replaced by parent script using sed
@@ -20,7 +21,7 @@ if [[ -n $TMPDIR ]]; then
 else
     TEMPDIR="$VERITAS_USER_DATA_DIR/TMPDIR/ANASUM-$(uuidgen)"
 fi
-mkdir -p $TEMPDIR
+mkdir -p "$TEMPDIR"
 echo "TEMPDIR: $TEMPDIR"
 
 getNumberedDirectory()
@@ -32,7 +33,7 @@ getNumberedDirectory()
     else
         ODIR="${IDIR}/${TRUN:0:2}/"
     fi
-    echo ${ODIR}
+    echo "${ODIR}"
 }
 
 # copy file list, runparameter and time masks file to tmp disk
@@ -53,7 +54,7 @@ for R in $RUNS; do
     if [[ -e "$DDIR/$R.anasum.root" ]]; then
         cp -f -v "$DDIR/$R.anasum.root" "$TEMPDIR"
     else
-        FIL="$(getNumberedDirectory $R ${DDIR})/${R}.anasum.root"
+        FIL="$(getNumberedDirectory "$R" ${DDIR})/${R}.anasum.root"
         if [[ -e "$FIL" ]]; then
             cp -f -v "$FIL" "$TEMPDIR"
         else
@@ -71,7 +72,7 @@ fi
 # determine if this is a short or long run list
 # (use VERSION string to identify long run list)
 NV=$(grep -c "VERSION" ${RUNLIST})
-if [ $NV -eq 0 ]; then
+if [ "$NV" -eq 0 ]; then
     RUNLISTSTRING="-k"
 else
     RUNLISTSTRING="-l"
@@ -101,7 +102,7 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/anasum
+        ls -l "${EVNDISPSYS}"/bin/anasum
     fi
 }
 echo "TEMPDIR: ${TEMPDIR}"
@@ -115,28 +116,30 @@ echo "RUNP ${RUNP}"
 echo "OUTPUTDATAFILE ${OUTPUTDATAFILE}"
 echo "OUTPUTLOGFILE ${OUTPUTLOGFILE}"
 
-$EVNDISPSYS/bin/anasum \
+"$EVNDISPSYS"/bin/anasum \
     -i 1 \
-    ${RUNLISTSTRING} ${RUNLIST} \
-    -d ${TEMPDIR} \
-    -f ${RUNP} \
-    -o ${OUTPUTDATAFILE}.root 2>&1 | tee ${OUTPUTLOGFILE}
+    ${RUNLISTSTRING} "${RUNLIST}" \
+    -d "${TEMPDIR}" \
+    -f "${RUNP}" \
+    -o "${OUTPUTDATAFILE}".root 2>&1 | tee ${OUTPUTLOGFILE}
 
 # for Crab runs: print sensitivity estimate
-RUNINFO=$($EVNDISPSYS/bin/printRunParameter ${OUTPUTDATAFILE}.root -runinfo)
-TMPTARGET=$(echo $RUNINFO | cut -d\  -f7- )
+RUNINFO=$("$EVNDISPSYS"/bin/printRunParameter "${OUTPUTDATAFILE}".root -runinfo)
+TMPTARGET=$(echo "$RUNINFO" | cut -d\  -f7- )
 if [[ ${TMPTARGET} == "Crab" ]]; then
-    echo "========================== SENSITIVITY ESTIMATE ==========================" >> ${OUTFILE}.log
-    $EVNDISPSYS/bin/printCrabSensitivity ${OUTPUTDATAFILE}.root >> ${OUTFILE}.log
-    echo "========================== ==========================" >> ${OUTFILE}.log
+    {
+        echo "========================== SENSITIVITY ESTIMATE =========================="
+        "$EVNDISPSYS"/bin/printCrabSensitivity "${OUTPUTDATAFILE}".root
+        echo "========================== =========================="
+    } >> "${OUTFILE}.log"
 fi
 
-echo "$(inspect_executables)" >> ${OUTFILE}.log
+inspect_executables >> ${OUTFILE}.log
 
 # log file into root file
-$EVNDISPSYS/bin/logFile \
+"$EVNDISPSYS"/bin/logFile \
     anasumLog \
-    ${OUTPUTDATAFILE}.root \
-    ${OUTPUTDATAFILE}.log
+    "${OUTPUTDATAFILE}".root \
+    "${OUTPUTDATAFILE}".log
 
 exit
diff --git a/scripts/helper_scripts/ANALYSIS.anasum_sub.sh b/scripts/helper_scripts/ANALYSIS.anasum_sub.sh
index a3915f8..01fae23 100755
--- a/scripts/helper_scripts/ANALYSIS.anasum_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.anasum_sub.sh
@@ -2,6 +2,7 @@
 # script to analyse one run with anasum
 
 # set observatory environmental variables
+# shellcheck source=/dev/null
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
@@ -48,7 +49,7 @@ if [[ -n "$TMPDIR" ]]; then
 else
     TEMPDIR="$VERITAS_USER_DATA_DIR/TMPDIR/MSCWDISP-$(uuidgen)"
 fi
-mkdir -p $TEMPDIR
+mkdir -p "$TEMPDIR"
 
 # explicit binding for apptainers
 if [ -n "$EVNDISP_APPTAINER" ]; then
@@ -79,7 +80,7 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/anasum
+        ls -l "${EVNDISPSYS}"/bin/anasum
     fi
 }
 
@@ -121,15 +122,15 @@ if [[ $FLIST == "NOTDEFINED" ]]; then
     echo "* VERSION 6" > $FLIST
     echo "" >> $FLIST
     # preparing effective area and radial acceptance names
-    RUNINFO=$($EVNDISPSYS/bin/printRunParameter "$INFILEPATH" -runinfo)
-    EPOCH=`echo "$RUNINFO" | awk '{print $(1)}'`
-    MAJOREPOCH=`echo $RUNINFO | awk '{print $(2)}'`
-    ATMO=${FORCEDATMO:-`echo $RUNINFO | awk '{print $(3)}'`}
-    OBSL=$(echo $RUNINFO | awk '{print $4}')
-    TELTOANA=`echo $RUNINFO | awk '{print "T"$(5)}'`
+    RUNINFO=$("$EVNDISPSYS"/bin/printRunParameter "$INFILEPATH" -runinfo)
+    EPOCH=$(echo "$RUNINFO" | awk '{print $(1)}')
+    MAJOREPOCH=$(echo "$RUNINFO" | awk '{print $(2)}')
+    ATMO=${FORCEDATMO:-$(echo "$RUNINFO" | awk '{print $(3)}')}
+    OBSL=$(echo "$RUNINFO" | awk '{print $4}')
+    TELTOANA=$(echo "$RUNINFO" | awk '{print "T"$(5)}')
 
-    REPLACESIMTYPEEff=$(prepare_irf_string $EPOCH $OBSL $SIMTYPE 0)
-    REPLACESIMTYPERad=$(prepare_irf_string $EPOCH $OBSL $SIMTYPE 1)
+    REPLACESIMTYPEEff=$(prepare_irf_string "$EPOCH" "$OBSL" $SIMTYPE 0)
+    REPLACESIMTYPERad=$(prepare_irf_string "$EPOCH" "$OBSL" $SIMTYPE 1)
 
     echo "RUN $RUNNUM at epoch $EPOCH and atmosphere $ATMO (Telescopes $TELTOANA SIMTYPE $REPLACESIMTYPEEff $REPLACESIMTYPERad)"
     # do string replacements
@@ -205,18 +206,20 @@ RUNP="${TEMPDIR}/$(basename $RUNP)"
 
 #################################
 # run anasum
-$EVNDISPSYS/bin/anasum   \
-    -f $RUNP             \
-    -l $FLIST            \
+"$EVNDISPSYS"/bin/anasum   \
+    -f "$RUNP"             \
+    -l "$FLIST"            \
     -d $INDIR            \
     -o $OUTPUTDATAFILE   &> $OUTPUTLOGFILE
 
-echo "$(inspect_executables)" >> ${OUTPUTLOGFILE}
-echo "INDIR ${INDIR}" >> ${OUTPUTLOGFILE}
-echo "VERITAS_ANALYSIS_TYPE ${VERITAS_ANALYSIS_TYPE}" >> ${OUTPUTLOGFILE}
+{
+    inspect_executables
+    echo "INDIR ${INDIR}"
+    echo "VERITAS_ANALYSIS_TYPE ${VERITAS_ANALYSIS_TYPE}"
+} >> "${OUTPUTLOGFILE}"
 
 if [[ -e "$OUTPUTLOGFILE" ]]; then
-    $EVNDISPSYS/bin/logFile anasumLog "$OUTPUTDATAFILE" "$(dirname $OUTPUTDATAFILE)/$(basename $OUTPUTLOGFILE)"
+    "$EVNDISPSYS"/bin/logFile anasumLog "$OUTPUTDATAFILE" "$(dirname $OUTPUTDATAFILE)/$(basename $OUTPUTLOGFILE)"
 fi
 
 echo "RUN$RUNNUM ANPARLOG log file: $OUTPUTLOGFILE"
diff --git a/scripts/helper_scripts/ANALYSIS.dispXGB_sub.sh b/scripts/helper_scripts/ANALYSIS.dispXGB_sub.sh
index 90da6bc..a9a1a8a 100755
--- a/scripts/helper_scripts/ANALYSIS.dispXGB_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.dispXGB_sub.sh
@@ -58,27 +58,27 @@ getNumberedDirectory()
     else
         ODIR="${IDIR}/${TRUN:0:2}/"
     fi
-    echo ${ODIR}
+    echo "${ODIR}"
 }
 
 echo $RUN
-MSCW_FILE="$(getNumberedDirectory $RUN ${VERITAS_PREPROCESSED_DATA_DIR}${VERITAS_ANALYSIS_TYPE:0:2}/mscw)/$RUN.mscw.root"
+MSCW_FILE="$(getNumberedDirectory $RUN "${VERITAS_PREPROCESSED_DATA_DIR}""${VERITAS_ANALYSIS_TYPE:0:2}"/mscw)/$RUN.mscw.root"
 if [[ ! -e ${MSCW_FILE} ]]; then
     echo "File ${MSCW_FILE} not found. Exiting."
     exit
 fi
-RUNINFO=$($EVNDISPSYS/bin/printRunParameter ${MSCW_FILE} -runinfo)
+RUNINFO=$("$EVNDISPSYS"/bin/printRunParameter "${MSCW_FILE}" -runinfo)
 echo "RUNINFO $RUNINFO"
-ZA=$(echo $RUNINFO | awk '{print $8}')
-EPOCH=$(echo $RUNINFO | awk '{print $1}')
-ATM=$(echo $RUNINFO | awk '{print $3}')
+ZA=$(echo "$RUNINFO" | awk '{print $8}')
+EPOCH=$(echo "$RUNINFO" | awk '{print $1}')
+ATM=$(echo "$RUNINFO" | awk '{print $3}')
 echo "MSCW file: ${MSCW_FILE} at zenith ${ZA} deg, epoch ${EPOCH}, ATM ${ATM}"
 DISPDIR="$VERITAS_EVNDISP_AUX_DIR/DispXGB/${ANATYPE}/${EPOCH}_ATM${ATM}"
 if [[ ! -d "${DISPDIR}" ]]; then
     echo "Error finding model directory $DISPDIR"
     exit
 fi
-OFIL=$(basename $MSCW_FILE .root)
+OFIL=$(basename "$MSCW_FILE" .root)
 if [[ "${XGB_TYPE}" == "stereo_analysis" ]]; then
     STEREO_PAR="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/XGB-stereo-parameter.json"
     BIN_ID=$(jq -r --arg za "$ZA" '
diff --git a/scripts/helper_scripts/ANALYSIS.evndisp_laser_sub.sh b/scripts/helper_scripts/ANALYSIS.evndisp_laser_sub.sh
index a89cbb6..6046daa 100755
--- a/scripts/helper_scripts/ANALYSIS.evndisp_laser_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.evndisp_laser_sub.sh
@@ -1,8 +1,9 @@
 #!/bin/bash
 # script to analyse laser files
 
+# shellcheck source=/dev/null
 # set observatory environmental variables
-source $EVNDISPSYS/setObservatory.sh VTS
+source "$EVNDISPSYS"/setObservatory.sh VTS
 
 # parameters replaced by parent script using sed
 RUN=RUNFILE
@@ -12,6 +13,6 @@ echo $RUN
 
 # run eventdisplay
 rm -f "$LOGDIR/$RUN.laser.log"
-${EVNDISPSCRIPTS}/SPANALYSIS.evndisp_laser_run.sh $RUN $TELTOANA &> $LOGDIR/$RUN.laser.log
+"${EVNDISPSCRIPTS}"/SPANALYSIS.evndisp_laser_run.sh $RUN $TELTOANA &> $LOGDIR/$RUN.laser.log
 
 exit
diff --git a/scripts/helper_scripts/ANALYSIS.evndisp_sub.sh b/scripts/helper_scripts/ANALYSIS.evndisp_sub.sh
index 506d3c5..de56d4c 100755
--- a/scripts/helper_scripts/ANALYSIS.evndisp_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.evndisp_sub.sh
@@ -2,6 +2,7 @@
 # script to analyse VTS raw files (VBF) with eventdisplay
 
 # set observatory environmental variables
+# shellcheck source=/dev/null
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
@@ -57,7 +58,7 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/evndisp
+        ls -l "${EVNDISPSYS}"/bin/evndisp
     fi
 }
 
@@ -73,8 +74,8 @@ unpack_db_textdirectory()
     DBRUNFIL="${DBTEXTDIRECTORY}/${SRUN}/${RRUN}.tar.gz"
     echo "DBTEXT FILE for $RRUN $DBRUNFIL" >&2
     if [[ -e ${DBRUNFIL} ]]; then
-        mkdir -p ${TMP_DBTEXTDIRECTORY}/${SRUN}
-        tar -xzf ${DBRUNFIL} -C ${TMP_DBTEXTDIRECTORY}/${SRUN}/ || return 1
+        mkdir -p "${TMP_DBTEXTDIRECTORY}"/"${SRUN}"
+        tar -xzf "${DBRUNFIL}" -C "${TMP_DBTEXTDIRECTORY}"/"${SRUN}"/ || return 1
     else
         echo "DBTEXT FILE not found ($DBRUNFIL)" >&2
         return 1
@@ -104,18 +105,18 @@ sub_dir()
 if [[ "${DBTEXTDIRECTORY}" != "0" ]]; then
     echo "UNPACKING DBTEXT from $RUN ${DBTEXTDIRECTORY}"
     TMP_DBTEXTDIRECTORY="${TEMPDIR}/DBTEXT"
-    TMP_LASERRUN=$(unpack_db_textdirectory $RUN $TMP_DBTEXTDIRECTORY)
+    TMP_LASERRUN=$(unpack_db_textdirectory $RUN "$TMP_DBTEXTDIRECTORY")
     if [[ $? -ne 0 || ! -r ${TMP_LASERRUN} ]]; then
         echo "failed to unpack DBTEXT laser-run metadata for run $RUN" >&2
         exit 1
     fi
-    LRUNID=$(cat ${TMP_LASERRUN} | grep -v run_id | awk -F "|" '{print $1}')
+    LRUNID=$(cat "${TMP_LASERRUN}" | grep -v run_id | awk -F "|" '{print $1}')
     for LL in ${LRUNID}
     do
         echo "  unpacking flasher/laser run: $LL"
-        unpack_db_textdirectory $LL $TMP_DBTEXTDIRECTORY >/dev/null || exit 1
+        unpack_db_textdirectory "$LL" "$TMP_DBTEXTDIRECTORY" >/dev/null || exit 1
     done
-    echo "DBTEXT directory $(ls -l $TMP_DBTEXTDIRECTORY)"
+    echo "DBTEXT directory $(ls -l "$TMP_DBTEXTDIRECTORY")"
 
     OPT=(-dbtextdirectory "${TMP_DBTEXTDIRECTORY}" -epochfile VERITAS.Epochs.runparameter)
     echo "${OPT[@]}"
@@ -135,7 +136,7 @@ get_run_date()
             done
         fi
         start_time="${a[$start_time_index]}"
-    done < ${OFIL}
+    done < "${OFIL}"
     year=$(date --utc -d "$start_time" +%Y)
     month=$(date --utc -d "$start_time" +%m)
     day=$(date --utc -d "$start_time" +%d)
@@ -146,14 +147,14 @@ get_run_date()
 #################################
 # check if run is on disk
 if [[ "${DBTEXTDIRECTORY}" != "0" ]]; then
-    RUNINFO=$(sub_dir ${TMP_DBTEXTDIRECTORY} ${RUN})/${RUN}/${RUN}.runinfo
+    RUNINFO=$(sub_dir "${TMP_DBTEXTDIRECTORY}" ${RUN})/${RUN}/${RUN}.runinfo
     if [[ ! -r ${RUNINFO} ]]; then
         echo "DBTEXT run info not readable (${RUNINFO})" >&2
         exit 1
     fi
-    RUNDATE=$(get_run_date ${RUNINFO})
+    RUNDATE=$(get_run_date "${RUNINFO}")
     echo "RUN $RUN $RUNINFO $RUNDATE"
-    ls -l ${TMP_DBTEXTDIRECTORY}
+    ls -l "${TMP_DBTEXTDIRECTORY}"
     # preference to VERITAS_DATA_DIR_2
     if [[ -e ${VERITAS_DATA_DIR_2}/data/${RUNDATE}/${RUN}.cvbf ]]; then
         if [ -n "$EVNDISP_APPTAINER" ]; then
@@ -172,7 +173,7 @@ if [[ "${DBTEXTDIRECTORY}" != "0" ]]; then
     fi
 else
     # original way accessing the VERITAS DB
-    RUNONDISK=$(echo $RUN | $EVNDISPSCRIPTS/RUNLIST.whichRunsAreOnDisk.sh -d)
+    RUNONDISK=$(echo $RUN | "$EVNDISPSCRIPTS"/RUNLIST.whichRunsAreOnDisk.sh -d)
 fi
 if [[ ${RUNONDISK} == *"file not found"** ]]; then
   echo "$RUN not on disk"
@@ -196,12 +197,12 @@ fi
 # pedestal calculation
 if [[ $CALIB == "1" || $CALIB == "2" || $CALIB == "4" || $CALIB == "5" ]]; then
     rm -f $LOGDIR/$RUN.ped.log
-    $EVNDISPSYS/bin/evndisp \
+    "$EVNDISPSYS"/bin/evndisp \
         -runmode=1 -runnumber="$RUN" \
         -reconstructionparameter "$ACUTS" \
         "${OPT[@]}" \
         -calibrationdirectory "$CALDIR" &> "$LOGDIR/$RUN.ped.log"
-    echo "$(inspect_executables)" >> "$LOGDIR/$RUN.ped.log"
+    inspect_executables >> "$LOGDIR/$RUN.ped.log"
     echo "RUN$RUN PEDLOG $LOGDIR/$RUN.ped.log"
 fi
 
@@ -228,13 +229,13 @@ fi
 # average tzero calculation
 if [[ $CALIB == "1" || $CALIB == "3" || $CALIB == "4" || $CALIB == "5" ]]; then
     rm -f $LOGDIR/$RUN.tzero.log
-    $EVNDISPSYS/bin/evndisp \
+    "$EVNDISPSYS"/bin/evndisp \
         -runnumber=$RUN -runmode=7 \
         -calibrationsummin=50 \
         -reconstructionparameter "$ACUTS" \
         "${OPT[@]}" \
         -calibrationdirectory "$CALDIR" &> "$LOGDIR/$RUN.tzero.log"
-    echo "$(inspect_executables)" >> "$LOGDIR/$RUN.tzero.log"
+    inspect_executables >> "$LOGDIR/$RUN.tzero.log"
     echo "RUN$RUN TZEROLOG $LOGDIR/$RUN.tzero.log"
 fi
 
@@ -263,31 +264,31 @@ fi
 if [[ $CALIB != "5" ]]; then
 LOGFILE="$LOGDIR/$RUN.log"
     rm -f "$LOGDIR/$RUN.log"
-    $EVNDISPSYS/bin/evndisp \
+    "$EVNDISPSYS"/bin/evndisp \
         -runnumber="$RUN" \
         -reconstructionparameter "$ACUTS" \
         -outputfile "$TEMPDIR/$RUN.root" \
         "${OPT[@]}" \
         -calibrationdirectory "$CALDIR" &> "$LOGFILE"
-    echo "$(inspect_executables)" >> "$LOGFILE"
+    inspect_executables >> "$LOGFILE"
     echo "RUN$RUN EVNDISPLOG $LOGFILE"
 fi
 
 # move log file into root file
 if [[ -e "$LOGFILE" ]]; then
-    cp -v $LOGFILE $TEMPDIR
+    cp -v "$LOGFILE" "$TEMPDIR"
     LLF="${TEMPDIR}/$RUN.log"
-    $EVNDISPSYS/bin/logFile evndispLog "$TEMPDIR/$RUN.root" "$LLF"
+    "$EVNDISPSYS"/bin/logFile evndispLog "$TEMPDIR/$RUN.root" "$LLF"
 fi
 if [[ -e "$LOGDIR/$RUN.ped.log" ]]; then
-    cp -v $LOGDIR/$RUN.ped.log $TEMPDIR
+    cp -v $LOGDIR/$RUN.ped.log "$TEMPDIR"
     LLF="${TEMPDIR}/$RUN.ped.log"
-    $EVNDISPSYS/bin/logFile evndisppedLog "$TEMPDIR/$RUN.root" "$LLF"
+    "$EVNDISPSYS"/bin/logFile evndisppedLog "$TEMPDIR/$RUN.root" "$LLF"
 fi
 if [[ -e "$LOGDIR/$RUN.tzero.log" ]]; then
-    cp -v $LOGDIR/$RUN.tzero.log $TEMPDIR
+    cp -v $LOGDIR/$RUN.tzero.log "$TEMPDIR"
     LLF="${TEMPDIR}/$RUN.tzero.log"
-    $EVNDISPSYS/bin/logFile evndisptzeroLog "$TEMPDIR/$RUN.root" "$LLF"
+    "$EVNDISPSYS"/bin/logFile evndisptzeroLog "$TEMPDIR/$RUN.root" "$LLF"
 fi
 
 # move data file from tmp dir to data dir
diff --git a/scripts/helper_scripts/ANALYSIS.mscw_energy_sub.sh b/scripts/helper_scripts/ANALYSIS.mscw_energy_sub.sh
index 4e3356a..2e432e9 100755
--- a/scripts/helper_scripts/ANALYSIS.mscw_energy_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.mscw_energy_sub.sh
@@ -2,6 +2,7 @@
 # analyse MC files with lookup tables
 
 # set observatory environmental variables
+# shellcheck source=/dev/null
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
@@ -33,8 +34,8 @@ if [[ ! -z  $VERITAS_ANALYSIS_TYPE ]]; then
    ANATYPE="${VERITAS_ANALYSIS_TYPE:0:2}"
 fi
 
-INDIR=`dirname $INFILE`
-BFILE=`basename $INFILE .root`
+INDIR=$(dirname $INFILE)
+BFILE=$(basename $INFILE .root)
 INFILEPATH="$INFILE"
 
 # temporary directory
@@ -66,10 +67,10 @@ if [ -n "$EVNDISP_APPTAINER" ]; then
 fi
 
 echo "READING RUNINFO from $INFILEPATH"
-RUNINFO=$($EVNDISPSYS/bin/printRunParameter $INFILEPATH updated-runinfo)
-EPOCH=`echo $RUNINFO | awk '{print $(1)}'`
-ATMO=${FORCEDATMO:-`echo $RUNINFO | awk '{print $(3)}'`}
-HVSETTINGS=`echo $RUNINFO | awk '{print $(4)}'`
+RUNINFO=$("$EVNDISPSYS"/bin/printRunParameter "$INFILEPATH" updated-runinfo)
+EPOCH=$(echo "$RUNINFO" | awk '{print $(1)}')
+ATMO=${FORCEDATMO:-$(echo "$RUNINFO" | awk '{print $(3)}')}
+HVSETTINGS=$(echo "$RUNINFO" | awk '{print $(4)}')
 if [[ $ATMO == *error* ]]; then
     echo "error finding atmosphere; skipping run $BFILE"
     exit
@@ -97,7 +98,7 @@ fi
 TABFILE=table-${IRFVERSION}-auxv01-${SIMTYPE_RUN}-ATM${ATMO}-${EPOCH}-${ANATYPE}.root
 echo "TABLEFILE: $TABFILE"
 # Check that table file exists
-if [[ "$TABFILE" == $(basename $TABFILE) ]]; then
+if [[ "$TABFILE" == $(basename "$TABFILE") ]]; then
     TABFILE="$VERITAS_EVNDISP_AUX_DIR/Tables/$TABFILE"
 fi
 echo "TABLEFILE $TABFILE"
@@ -106,7 +107,7 @@ if [ ! -f "$TABFILE" ]; then
     exit 1
 fi
 if [ -n "$EVNDISP_APPTAINER" ]; then
-    TABFILE="/opt/VERITAS_EVNDISP_AUX_DIR/Tables/$(basename $TABFILE)"
+    TABFILE="/opt/VERITAS_EVNDISP_AUX_DIR/Tables/$(basename "$TABFILE")"
 fi
 
 inspect_executables()
@@ -114,7 +115,7 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/mscw_energy
+        ls -l "${EVNDISPSYS}"/bin/mscw_energy
     fi
 }
 
@@ -153,9 +154,9 @@ get_disp_dir()
 }
 
 if [[ $DISPBDT == "1" ]]; then
-    ZA=$($EVNDISPSYS/bin/printRunParameter $INFILEPATH -zenith | awk '{print $4}')
-    DISPDIR=$(get_disp_dir ${ZA})
-    echo "DISPDIR (Zenith is $ZA deg): " $DISPDIR
+    ZA=$("$EVNDISPSYS"/bin/printRunParameter "$INFILEPATH" -zenith | awk '{print $4}')
+    DISPDIR=$(get_disp_dir "${ZA}")
+    echo "DISPDIR (Zenith is $ZA deg): " "$DISPDIR"
     if [[ ! -d "$DISPDIR" ]]; then
         echo "Error: DispBDT directory $DISPDIR not found, exiting..."
         exit 1
@@ -166,73 +167,91 @@ fi
 # run analysis
 
 MSCWLOGFILE="$ODIR/$BFILE.mscw.log"
-rm -f ${MSCWLOGFILE}
+rm -f "${MSCWLOGFILE}"
 
 MSCWDATAFILE="$ODIR/$BFILE.mscw.root"
 echo "MSCWDATAFILE $MSCWDATAFILE"
 
 # mscw_energy command line options
-MOPT=""
+MOPT=()
 # dispBDT reconstruction
 if [ $DISPBDT -eq 1 ]; then
-    MOPT="$MOPT -redo_stereo_reconstruction"
-    MOPT="$MOPT -tmva_disperror_weight 50"
-    MOPT="$MOPT -minangle_stereo_reconstruction=10."
+    MOPT+=(
+        -redo_stereo_reconstruction
+        -tmva_disperror_weight
+        50
+        -minangle_stereo_reconstruction=10.
+    )
     if [[ $IRFVERSION == v490* ]]; then
-        MOPT="$MOPT -maxloss=0.20"
+        MOPT+=("-maxloss=0.20")
     else
-        MOPT="$MOPT -maxdist=1.75 -minntubes=5 -minwidth=0.02 -minsize=100"
-        MOPT="$MOPT -maxloss=0.40"
-        MOPT="$MOPT -use_evndisp_selected_images=0"
+        MOPT+=(
+            -maxdist=1.75
+            -minntubes=5
+            -minwidth=0.02
+            -minsize=100
+            -maxloss=0.40
+            -use_evndisp_selected_images=0
+        )
     fi
-    # MOPT="$MOPT -minfui=0.2"
-    # MOPT="$MOPT -minfitstat=3"
+    # MOPT+=("-minfui=0.2")
+    # MOPT+=("-minfitstat=3")
     # unzip XML files into DDIR
-    cp -v -f ${DISPDIR}/*.xml.gz ${DDIR}/
-    gunzip -v ${DDIR}/*xml.gz
-    MOPT="$MOPT -tmva_filename_stereo_reconstruction ${DDIR}/BDTDisp_BDT_"
-    MOPT="$MOPT -tmva_filename_disperror_reconstruction ${DDIR}/BDTDispError_BDT_"
-    MOPT="$MOPT -tmva_filename_dispsign_reconstruction ${DDIR}/BDTDispSign_BDT_"
+    cp -v -f "${DISPDIR}"/*.xml.gz "${DDIR}"/
+    gunzip -v "${DDIR}"/*xml.gz
+    MOPT+=(
+        -tmva_filename_stereo_reconstruction
+        "${DDIR}/BDTDisp_BDT_"
+        -tmva_filename_disperror_reconstruction
+        "${DDIR}/BDTDispError_BDT_"
+        -tmva_filename_dispsign_reconstruction
+        "${DDIR}/BDTDispSign_BDT_"
+    )
     if [[ $IRFVERSION != v490* ]]; then
-        MOPT="$MOPT -tmva_filename_energy_reconstruction ${DDIR}/BDTDispEnergy_BDT_"
+        MOPT+=(
+            -tmva_filename_energy_reconstruction
+            "${DDIR}/BDTDispEnergy_BDT_"
+        )
     fi
-    echo "DISP BDT options: $MOPT"
+    echo "DISP BDT options: ${MOPT[*]}"
 fi
 
-$EVNDISPSYS/bin/mscw_energy         \
-    ${MOPT} \
+"$EVNDISPSYS"/bin/mscw_energy         \
+    "${MOPT[@]}" \
     -updateEpoch=1 \
-    -tablefile $TABFILE             \
+    -tablefile "$TABFILE"             \
     -arrayrecid=$RECID              \
-    -inputfile $DDIR/$BFILE.root \
-    -writeReconstructedEventsOnly=1 &> ${MSCWLOGFILE}
+    -inputfile "$DDIR"/"$BFILE".root \
+    -writeReconstructedEventsOnly=1 &> "${MSCWLOGFILE}"
 
-echo "$(inspect_executables)" >> ${MSCWLOGFILE}
+inspect_executables >> "${MSCWLOGFILE}"
 
 # write DISP directory into log file (as tmp directories are used)
 if [[ $DISPBDT != "NOTSET" ]]; then
-    echo "" >> ${MSCWLOGFILE}
-    echo "dispBDT XML files read from ${DISPDIR}" >> ${MSCWLOGFILE}
+    echo "" >> "${MSCWLOGFILE}"
+    echo "dispBDT XML files read from ${DISPDIR}" >> "${MSCWLOGFILE}"
 fi
-echo "EVNDISP file: ${INFILE}" >> ${MSCWLOGFILE}
-echo "VERITAS_EVNDISP_AUX: ${VERITAS_EVNDISP_AUX_DIR}" >> ${MSCWLOGFILE}
-echo "VERITAS_ANALYSIS_TYPE ${VERITAS_ANALYSIS_TYPE}" >> ${MSCWLOGFILE}
+{
+    echo "EVNDISP file: ${INFILE}"
+    echo "VERITAS_EVNDISP_AUX: ${VERITAS_EVNDISP_AUX_DIR}"
+    echo "VERITAS_ANALYSIS_TYPE ${VERITAS_ANALYSIS_TYPE}"
+} >> "${MSCWLOGFILE}"
 
 # move logfiles into output file
 if [[ -e ${MSCWLOGFILE} ]]; then
-  cp -v ${MSCWLOGFILE} $DDIR/
-  LLF="${DDIR}/$(basename ${MSCWLOGFILE})"
-  $EVNDISPSYS/bin/logFile mscwTableLog "$DDIR/$BFILE.mscw.root" "$LLF"
+  cp -v "${MSCWLOGFILE}" "$DDIR"/
+  LLF="${DDIR}/$(basename "${MSCWLOGFILE}")"
+  "$EVNDISPSYS"/bin/logFile mscwTableLog "$DDIR/$BFILE.mscw.root" "$LLF"
 fi
 
 # move output file from scratch and clean up
-cp -f -v $DDIR/$BFILE.mscw.root $MSCWDATAFILE
-rm -f $DDIR/$BFILE.mscw.root
-rm -f $DDIR/$BFILE.root
+cp -f -v "$DDIR"/"$BFILE".mscw.root "$MSCWDATAFILE"
+rm -f "$DDIR"/"$BFILE".mscw.root
+rm -f "$DDIR"/"$BFILE".root
 
 # write info to log
 echo "RUN$BFILE MSCWLOG ${MSCWLOGFILE}"
 echo "RUN$BFILE MSCWDATA $MSCWDATAFILE"
 
 # remove files in DDIR
-rm -rf $DDIR
+rm -rf "$DDIR"
diff --git a/scripts/helper_scripts/ANALYSIS.v2dl3_sub.sh b/scripts/helper_scripts/ANALYSIS.v2dl3_sub.sh
index c4b9136..4a44aa1 100755
--- a/scripts/helper_scripts/ANALYSIS.v2dl3_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.v2dl3_sub.sh
@@ -22,8 +22,8 @@ echo "Scratch dir: $TEMPDIR"
 mkdir -p "$TEMPDIR"
 
 # run list
-FILES=`cat "$RUNLIST"`
-NRUNS=`cat "$RUNLIST" | wc -l `
+FILES=$(cat "$RUNLIST")
+NRUNS=$(cat "$RUNLIST" | wc -l )
 echo "total number of runs to analyze: $NRUNS"
 echo
 
@@ -52,19 +52,24 @@ check_conda_installation()
 }
 
 check_conda_installation
+# shellcheck source=/dev/null
 
 source activate base
 conda activate v2dl3Eventdisplay-${V2DL3VERSION}
 # Install only if not already present (avoid slow per-job reinstall)
 pip show v2dl3-eventdisplay &>/dev/null 2>&1 || pip install -e "${V2DL3SYS%/}-v${V2DL3VERSION}"
 
-V2DL3OPT="--fuzzy_boundary zenith 0.05 --fuzzy_boundary pedvar 0.5 --save_multiplicity"
+V2DL3OPT=(
+    --fuzzy_boundary zenith 0.05
+    --fuzzy_boundary pedvar 0.5
+    --save_multiplicity
+)
 # selection for full-gamma files
 EVENTFILTER="${TEMPDIR}/tmp_select.yml"
-echo "IsGamma: 1" > $EVENTFILTER
+echo "IsGamma: 1" > "$EVENTFILTER"
 echo "Event filter file: ${EVENTFILTER}"
-ls -l ${EVENTFILTER}
-cat ${EVENTFILTER}
+ls -l "${EVENTFILTER}"
+cat "${EVENTFILTER}"
 
 # directory schema for preprocessed files
 getNumberedDirectory()
@@ -76,7 +81,7 @@ getNumberedDirectory()
     else
         ODIR="${IDIR}/${TRUN:0:2}/"
     fi
-    echo ${ODIR}
+    echo "${ODIR}"
 }
 
 # interpolator; might depend on IRF type
@@ -99,20 +104,20 @@ getInterpolator()
 
 for RUN in $FILES
 do
-    echo $RUN
-    ANASUMFILE="$(getNumberedDirectory $RUN $VERITAS_PREPROCESSED_DATA_DIR/${VERITAS_ANALYSIS_TYPE:0:2}/anasum_${CUT})/${RUN}.anasum.root"
+    echo "$RUN"
+    ANASUMFILE="$(getNumberedDirectory "$RUN" "$VERITAS_PREPROCESSED_DATA_DIR"/"${VERITAS_ANALYSIS_TYPE:0:2}"/anasum_${CUT})/${RUN}.anasum.root"
     if [[ ! -e ${ANASUMFILE} ]]; then
         echo "File ${ANASUMFILE} not found"
         echo "Skipping run $RUN"
         continue
     fi
     echo "   ANASUM file: ${ANASUMFILE}"
-    result=$(v2dl3-eventdisplay-query-runparameters ${ANASUMFILE} ${RUN})
-    EPOCH=$(echo $result |  awk '{print $2}')
-    EFFAREA=$(echo $result | awk '{print $5}')
+    result=$(v2dl3-eventdisplay-query-runparameters "${ANASUMFILE}" "${RUN}")
+    EPOCH=$(echo "$result" |  awk '{print $2}')
+    EFFAREA=$(echo "$result" | awk '{print $5}')
     echo "   Effective area file: $EFFAREA Epoch: $EPOCH"
-    DBFITSFILE=$(getNumberedDirectory $RUN $VERITAS_DATA_DIR/shared/DBFITS)/$RUN.db.fits.gz
-    INTERPOLATOR=$(getInterpolator $EFFAREA)
+    DBFITSFILE=$(getNumberedDirectory "$RUN" "$VERITAS_DATA_DIR"/shared/DBFITS)/$RUN.db.fits.gz
+    INTERPOLATOR=$(getInterpolator "$EFFAREA")
     if [[ ! -e ${DBFITSFILE} ]]; then
         echo "DB File ${DBFITSFILE} not found"
         echo "Skipping run $RUN"
@@ -122,33 +127,33 @@ do
 
     for m in "point-like" "full-enclosure"
     do
-        echo "   Converting (${m}, ${V2DL3OPT})"
+        echo "   Converting (${m}, ${V2DL3OPT[*]})"
 
         for p in "" "-all-events"
         do
             if [[ "$p" != "-all-events" ]]; then
-                V2DL3SELECT="--evt_filter ${EVENTFILTER}"
-                ls -1 ${EVENTFILTER}
+                V2DL3SELECT=(--evt_filter "${EVENTFILTER}")
+                ls -1 "${EVENTFILTER}"
             else
-                V2DL3SELECT=""
+                V2DL3SELECT=()
             fi
-            echo "EVENTFILTER $V2DL3SELECT"
+            echo "EVENTFILTER ${V2DL3SELECT[*]}"
 
             mkdir -p ${ODIR}/${m}${p}
-            rm -f ${ODIR}/${m}${p}/${RUN}.log
+            rm -f ${ODIR}/${m}${p}/"${RUN}".log
 
             v2dl3-eventdisplay \
                 --${m} \
-                ${V2DL3OPT} ${V2DL3SELECT} \
-                --file_pair ${ANASUMFILE} $VERITAS_EVNDISP_AUX_DIR/EffectiveAreas/${EFFAREA} \
-                --logfile ${ODIR}/${m}${p}/${RUN}.log \
-                --instrument_epoch ${EPOCH} \
-                --interpolator_name ${INTERPOLATOR} \
-                --db_fits_file ${DBFITSFILE} \
-                ${ODIR}/${m}${p}/${RUN}.fits.gz
-
-            python --version >> ${ODIR}/${m}${p}/${RUN}.log
-            conda list -n v2dl3Eventdisplay-${V2DL3VERSION} >> ${ODIR}/${m}${p}/${RUN}.log
+                "${V2DL3OPT[@]}" "${V2DL3SELECT[@]}" \
+                --file_pair "${ANASUMFILE}" "$VERITAS_EVNDISP_AUX_DIR"/EffectiveAreas/"${EFFAREA}" \
+                --logfile ${ODIR}/${m}${p}/"${RUN}".log \
+                --instrument_epoch "${EPOCH}" \
+                --interpolator_name "${INTERPOLATOR}" \
+                --db_fits_file "${DBFITSFILE}" \
+                ${ODIR}/${m}${p}/"${RUN}".fits.gz
+
+            python --version >> ${ODIR}/${m}${p}/"${RUN}".log
+            conda list -n v2dl3Eventdisplay-${V2DL3VERSION} >> ${ODIR}/${m}${p}/"${RUN}".log
             PDIR=$(pwd)
             cd "${PDIR}" || exit
         done
diff --git a/scripts/helper_scripts/IRF.compress_evndisp_MC_sub.sh b/scripts/helper_scripts/IRF.compress_evndisp_MC_sub.sh
index c2003a9..f82b81f 100755
--- a/scripts/helper_scripts/IRF.compress_evndisp_MC_sub.sh
+++ b/scripts/helper_scripts/IRF.compress_evndisp_MC_sub.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 # script put log files into evndisp file and compress output
 
+# shellcheck source=/dev/null
 # set observatory environmental variables
 source "$EVNDISPSYS"/setObservatory.sh VTS
 
@@ -15,28 +16,28 @@ else
     DDIR="/tmp/testDir"
 fi
 DDIR=${DDIR}/$(uuidgen)
-mkdir -p $DDIR
+mkdir -p "$DDIR"
 mkdir -p $ODIR
 
 compare_log_file()
 {
-    $EVNDISPSYS/bin/logFile $1 $DDIR/$ONAME.root > ${DDIR}/${1}.log
+    "$EVNDISPSYS"/bin/logFile "$1" "$DDIR"/$ONAME.root > "${DDIR}"/"${1}".log
     if cmp -s "${2}" "${DDIR}/${1}.log"; then
         echo "FILES ${1} ${2} are the same, removing"
     else
-        touch $ODIR/$ONAME.${1}.errorlog
-        echo "Error, ${1} ${2} differ" >> $ODIR/$ONAME.${1}.errorlog
+        touch $ODIR/$ONAME."${1}".errorlog
+        echo "Error, ${1} ${2} differ" >> $ODIR/$ONAME."${1}".errorlog
     fi
 }
 
 add_log_file()
 {
      # first check if logFile is already included in evndisp file
-     LCON=$($EVNDISPSYS/bin/logFile $1 $DDIR/$ONAME.root | grep "Error: log file object" | wc -l)
+     LCON=$("$EVNDISPSYS"/bin/logFile "$1" "$DDIR"/$ONAME.root | grep -c "Error: log file object")
      if [[ ${LCON} == 1 ]]; then
          echo "writing log file ${2}"
          if [[ -f ${2} ]]; then
-             $EVNDISPSYS/bin/logFile $1 $DDIR/$ONAME.root ${2}
+             "$EVNDISPSYS"/bin/logFile "$1" "$DDIR"/$ONAME.root "${2}"
          fi
      else
          echo "log file ${2} already in $DDIR/$ONAME.root"
@@ -46,8 +47,8 @@ add_log_file()
 compress_file()
 {
     if command -v zstd &>/dev/null; then
-        zstd ${1}
-        zstd --test ${1}.zst
+        zstd "${1}"
+        zstd --test "${1}".zst
     else
         echo "Error: zstd compressing executable not found"
         exit
@@ -57,7 +58,7 @@ compress_file()
 
 echo "EVNDISP input root file $IDIR/$ONAME.root"
 echo "EVNDISP output root file $ODIR/$ONAME.root.zst"
-cp -v $IDIR/$ONAME.root ${DDIR}/
+cp -v $IDIR/$ONAME.root "${DDIR}"/
 
 ### add log files to evndisp file
 add_log_file evndispLog $IDIR/$ONAME.log
@@ -69,5 +70,5 @@ compare_log_file evndispLog $IDIR/$ONAME.log
 compare_log_file evndisppedLog $IDIR/$ONAME.ped.log
 compare_log_file evndisptzeroLog $IDIR/$ONAME.tzero.log
 
-compress_file $DDIR/$ONAME.root
-mv -f -v $DDIR/$ONAME.root.zst ${ODIR}/
+compress_file "$DDIR"/$ONAME.root
+mv -f -v "$DDIR"/$ONAME.root.zst ${ODIR}/
diff --git a/scripts/helper_scripts/IRF.dispXGB_sub.sh b/scripts/helper_scripts/IRF.dispXGB_sub.sh
index bce4a3f..36b6671 100755
--- a/scripts/helper_scripts/IRF.dispXGB_sub.sh
+++ b/scripts/helper_scripts/IRF.dispXGB_sub.sh
@@ -57,11 +57,11 @@ if [[ ! -e ${MSCW_FILE} ]]; then
     echo "File ${MSCW_FILE} not found. Exiting."
     exit
 fi
-RUNINFO=$($EVNDISPSYS/bin/printRunParameter ${MSCW_FILE} -runinfo)
+RUNINFO=$("$EVNDISPSYS"/bin/printRunParameter ${MSCW_FILE} -runinfo)
 echo "RUNINFO $RUNINFO"
-ZA=$(echo $RUNINFO | awk '{print $8}')
-EPOCH=$(echo $RUNINFO | awk '{print $1}')
-ATM=$(echo $RUNINFO | awk '{print $3}')
+ZA=$(echo "$RUNINFO" | awk '{print $8}')
+EPOCH=$(echo "$RUNINFO" | awk '{print $1}')
+ATM=$(echo "$RUNINFO" | awk '{print $3}')
 echo "MSCW file: ${MSCW_FILE} at zenith ${ZA} deg, epoch ${EPOCH}, ATM ${ATM}"
 DISPDIR="$VERITAS_EVNDISP_AUX_DIR/DispXGB/${ANATYPE}/${EPOCH}_ATM${ATM}"
 if [[ ! -d "${DISPDIR}" ]]; then
diff --git a/scripts/helper_scripts/IRF.effective_area_combine_sub.sh b/scripts/helper_scripts/IRF.effective_area_combine_sub.sh
index 281331c..ab5d1dd 100755
--- a/scripts/helper_scripts/IRF.effective_area_combine_sub.sh
+++ b/scripts/helper_scripts/IRF.effective_area_combine_sub.sh
@@ -1,9 +1,9 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # combine effective areas
 
 # set observatory environmental variables
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
+# shellcheck source=/dev/null
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
 
@@ -26,7 +26,6 @@ if [ -n "$EVNDISP_APPTAINER" ]; then
     EVNDISPSYS="${EVNDISPSYS/--cleanenv/--cleanenv $APPTAINER_ENV $APPTAINER_MOUNT}"
     echo "APPTAINER SYS: $EVNDISPSYS"
     # path used by EVNDISPSYS needs to be set
-    CALDIR="/opt/ODIR"
     DDIR="/opt/DDIR/"
     OPTODIR="/opt/ODIR/"
 fi
@@ -36,7 +35,7 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/evndisp
+        ls -l "${EVNDISPSYS}"/bin/evndisp
     fi
 }
 
@@ -46,14 +45,14 @@ chmod -R g+w $ODIR
 rm -f "$ODIR"/"$OFILE".list
 touch  "$ODIR"/"$OFILE".list
 for F in $EAFILES; do
-    AP_FILE=$(basename $F)
+    AP_FILE=$(basename "$F")
     echo "$DDIR/$AP_FILE" >> "$ODIR"/"$OFILE".list
 done
 echo "Found $(cat $ODIR/$OFILE.list | wc -l) input files to merge"
 echo "File list: $ODIR/$OFILE.list"
 
-$EVNDISPSYS/bin/combineEffectiveAreas "$OPTODIR/$OFILE.list" ${OPTODIR}/$OFILE DL3reduced &> ${ODIR}/$OFILE.log
+"$EVNDISPSYS"/bin/combineEffectiveAreas "$OPTODIR/$OFILE.list" ${OPTODIR}/$OFILE DL3reduced &> ${ODIR}/$OFILE.log
 
 # log files
-echo "$(inspect_executables)" >> "$ODIR/$OFILE.log"
-$EVNDISPSYS/bin/logFile effAreaCombineLog "${OPTODIR}/$OFILE.root" "${OPTODIR}/$OFILE.log"
+inspect_executables >> "$ODIR/$OFILE.log"
+"$EVNDISPSYS"/bin/logFile effAreaCombineLog "${OPTODIR}/$OFILE.root" "${OPTODIR}/$OFILE.log"
diff --git a/scripts/helper_scripts/IRF.effective_area_parallel_sub.sh b/scripts/helper_scripts/IRF.effective_area_parallel_sub.sh
index 119f231..3191f78 100755
--- a/scripts/helper_scripts/IRF.effective_area_parallel_sub.sh
+++ b/scripts/helper_scripts/IRF.effective_area_parallel_sub.sh
@@ -1,11 +1,11 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # calculate effective areas
 #
 # v490: possible issue with "RERUN_STEREO_RECONSTRUCTION_3TEL" option
 
 # set observatory environmental variables
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
+# shellcheck source=/dev/null
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
 
@@ -42,7 +42,6 @@ if [ -n "$EVNDISP_APPTAINER" ]; then
     EVNDISPSYS="${EVNDISPSYS/--cleanenv/--cleanenv $APPTAINER_ENV $APPTAINER_MOUNT}"
     echo "APPTAINER SYS: $EVNDISPSYS"
     # path used by EVNDISPSYS needs to be set
-    CALDIR="/opt/ODIR"
 fi
 
 inspect_executables()
@@ -50,7 +49,7 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/evndisp
+        ls -l "${EVNDISPSYS}"/bin/evndisp
     fi
 }
 
@@ -66,14 +65,14 @@ do
 done
 # cp MC file to TMPDIR
 cp -f -v "$MCFILE" "$DDIR"/
-MCFILE=`basename $MCFILE`
+MCFILE=$(basename $MCFILE)
 MCFILE=${DDIR}/${MCFILE}
 
 # Check that cuts file exists
 CUTSFILE=${CUTSFILE%%.dat}
-CUTS_NAME=`basename $CUTSFILE`
+CUTS_NAME=$(basename "$CUTSFILE")
 CUTS_NAME=${CUTS_NAME##ANASUM.GammaHadron-}
-if [[ "$CUTSFILE" == `basename $CUTSFILE` ]]; then
+if [[ "$CUTSFILE" == $(basename "$CUTSFILE") ]]; then
     CUTSFILE="$VERITAS_EVNDISP_AUX_DIR"/GammaHadronCutFiles/$CUTSFILE.dat
 else
     CUTSFILE="$CUTSFILE.dat"
@@ -89,7 +88,7 @@ if [[ $DISPBDT == "1" ]]; then
     OSUBDIR="${OSUBDIR}_DISP"
 fi
 echo -e "Output files will be written to:\n $OSUBDIR"
-mkdir -p $OSUBDIR
+mkdir -p "$OSUBDIR"
 
 ENERGYRECONSTRUCTIONMETHOD="0"
 if [[ $IRFVERSION == *"v490"* ]]; then
@@ -117,7 +116,7 @@ PARAMFILE="
 * FILLMONTECARLOHISTOS 0
 * ENERGYSPECTRUMINDEX 40 1.5 0.1
 * RERUN_STEREO_RECONSTRUCTION_3TEL $REDO3TEL
-* CUTFILE $DDIR/$(basename $CUTSFILE)
+* CUTFILE $DDIR/$(basename "$CUTSFILE")
  IGNOREFRACTIONOFEVENTS 0.5
 * SIMULATIONFILE_DATA $MCFILE
 * XGBSTEREOFILESUFFIX $XGBSTEREOFILESUFFIX
@@ -126,17 +125,17 @@ PARAMFILE="
 # create makeEffectiveArea parameter file
 EAPARAMS="$EFFAREAFILE-${CUTS_NAME}"
 rm -f "$DDIR/$EAPARAMS.dat"
-eval "echo \"$PARAMFILE\"" > $DDIR/$EAPARAMS.dat
+eval "echo \"$PARAMFILE\"" > "$DDIR"/"$EAPARAMS".dat
 
 # calculate effective areas
-rm -f $OSUBDIR/$OFILE.root
-$EVNDISPSYS/bin/makeEffectiveArea $DDIR/$EAPARAMS.dat $DDIR/$EAPARAMS.root &> $OSUBDIR/$EAPARAMS.log
+rm -f "$OSUBDIR"/"$OFILE".root
+"$EVNDISPSYS"/bin/makeEffectiveArea "$DDIR"/"$EAPARAMS".dat "$DDIR"/"$EAPARAMS".root &> "$OSUBDIR"/"$EAPARAMS".log
 
 echo "Filling log file into root file"
-echo "$(inspect_executables)" >> "$OSUBDIR/$EAPARAMS.log"
+inspect_executables >> "$OSUBDIR/$EAPARAMS.log"
 cp -v "$OSUBDIR/$EAPARAMS.log" "$DDIR/$EAPARAMS.log"
-$EVNDISPSYS/bin/logFile effAreaLog $DDIR/$EAPARAMS.root $DDIR/$EAPARAMS.log
-rm -f $OSUBDIR/$EAPARAMS.log
-cp -f $DDIR/$EAPARAMS.root $OSUBDIR/$EAPARAMS.root
-chmod -R g+w $OSUBDIR
-chmod g+w $OSUBDIR/$EAPARAMS.root
+"$EVNDISPSYS"/bin/logFile effAreaLog "$DDIR"/"$EAPARAMS".root "$DDIR"/"$EAPARAMS".log
+rm -f "$OSUBDIR"/"$EAPARAMS".log
+cp -f "$DDIR"/"$EAPARAMS".root "$OSUBDIR"/"$EAPARAMS".root
+chmod -R g+w "$OSUBDIR"
+chmod g+w "$OSUBDIR"/"$EAPARAMS".root
diff --git a/scripts/helper_scripts/IRF.evndisp_MC_sub.sh b/scripts/helper_scripts/IRF.evndisp_MC_sub.sh
index 5c12d48..f7e41ef 100755
--- a/scripts/helper_scripts/IRF.evndisp_MC_sub.sh
+++ b/scripts/helper_scripts/IRF.evndisp_MC_sub.sh
@@ -1,9 +1,10 @@
 #!/bin/bash
-# shellcheck disable=SC2034,SC2154
+# shellcheck disable=SC2154
 # script to run evndisp for simulations on one of the cluster nodes (VBF)
 
 # set observatory environmental variables
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
+# shellcheck source=/dev/null
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
 
@@ -11,14 +12,17 @@ fi
 RUNNUM="${1}"
 SIMDIR=DATADIR
 ZA=ZENITHANGLE
+# shellcheck disable=SC2034  # template placeholder, replaced by sed before job submission
 WOB=DECIMALWOBBLE
 WOG=INTEGERWOBBLE
 NOISE=NOISELEVEL
 EPOCH=ARRAYEPOCH
+# shellcheck disable=SC2034  # template placeholder, replaced by sed before job submission
 ATM=ATMOSPHERE
 ACUTS="RECONSTRUCTIONRUNPARAMETERFILE"
 SIMTYPE=SIMULATIONTYPE
 ODIR=OUTPUTDIR
+# shellcheck disable=SC2034  # template placeholder, replaced by sed before job submission
 TELTOANA="1234"
 VBFNAME="$2"
 NOISEFILE=NOISEFFILE
@@ -96,8 +100,8 @@ if [ -e "$V4N" ]; then
     for file in "$V4N"/*.root.zst; do
         tmpfile="$TMPDIR/$(basename "${file%.zst}")"
         zstd -d -c "$file" > "$tmpfile"
-        if $EVNDISPSYS/bin/logFile evndispLog "$tmpfile" | grep -q "$VBF_BASENAME"; then
-            echo "File $VBFNAME ($VBF_BASENAME) already processed ($(basename $tmpfile))"
+        if "$EVNDISPSYS"/bin/logFile evndispLog "$tmpfile" | grep -q "$VBF_BASENAME"; then
+            echo "File $VBFNAME ($VBF_BASENAME) already processed ($(basename "$tmpfile"))"
             exit
         fi
     done
@@ -113,7 +117,7 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/evndisp
+        ls -l "${EVNDISPSYS}"/bin/evndisp
     fi
 }
 
@@ -130,7 +134,11 @@ else
 fi
 
 # Amplitude correction factor options
-AMPCORR="-traceamplitudecorrection ThroughputCorrection.runparameter -pedestalDefaultPedestal=$PEDLEV"
+AMPCORR=(
+    -traceamplitudecorrection
+    ThroughputCorrection.runparameter
+    "-pedestalDefaultPedestal=$PEDLEV"
+)
 # CARE simulations: add Gaussian noise of 3.6 mV/ (7.84 mV/dc)  / 2
 # Current (2018) CARE simulations:
 #    no electronic noise included - therefore add
@@ -138,7 +146,7 @@ AMPCORR="-traceamplitudecorrection ThroughputCorrection.runparameter -pedestalDe
 #    Derived for GrIsu many years ago - source not entirely clear
 #    add Gaussian noise of 3.6 mV/ (7.84 mV/dc)  / 2
 if [[ ${SIMTYPE:0:4} == "CARE" ]]; then
-    AMPCORR="$AMPCORR -injectGaussianNoise=0.229592"
+    AMPCORR+=("-injectGaussianNoise=0.229592")
 fi
 
 # detector configuration
@@ -147,7 +155,7 @@ fi
 [[ ${EPOCH:0:2} == "V6" ]] && CFG="EVN_V6_Upgrade_20121127_v420.txt"
 
 CALDIR=${DDIR}
-mkdir -p ${CALDIR}/Calibration
+mkdir -p "${CALDIR}"/Calibration
 echo "Calibration directory: ${CALDIR}"
 
 ##################3
@@ -156,17 +164,17 @@ if [[ -f "${SIMDIR}/$VBFNAME" ]]; then
    ZTYPE=${VBFNAME##*.}
    if [[ $ZTYPE == "gz" ]]; then
        echo " (vbf is gzipped)"
-       VBF_FILE=$(basename $SIMDIR/${VBFNAME} .gz)
-       gunzip -f -q -c $SIMDIR/${VBFNAME} > ${DDIR}/${VBF_FILE}
+       VBF_FILE=$(basename $SIMDIR/"${VBFNAME}" .gz)
+       gunzip -f -q -c $SIMDIR/"${VBFNAME}" > "${DDIR}"/"${VBF_FILE}"
    elif [[ $ZTYPE == "bz2" ]]; then
        echo " (vbf is bzipped)"
-       VBF_FILE=$(basename $SIMDIR/${VBFNAME} .bz2)
-       bunzip2 -f -q -c $SIMDIR/${VBFNAME} > ${DDIR}/${VBF_FILE}
+       VBF_FILE=$(basename $SIMDIR/"${VBFNAME}" .bz2)
+       bunzip2 -f -q -c $SIMDIR/"${VBFNAME}" > "${DDIR}"/"${VBF_FILE}"
    elif [[ $ZTYPE == "zst" ]]; then
        echo " (vbf is zst-compressed)"
        if hash zstd 2>/dev/null; then
-           VBF_FILE=$(basename $SIMDIR/${VBFNAME} .zst)
-           zstd -d -f ${SIMDIR}/${VBFNAME} -o ${DDIR}/${VBF_FILE}
+           VBF_FILE=$(basename $SIMDIR/"${VBFNAME}" .zst)
+           zstd -d -f ${SIMDIR}/"${VBFNAME}" -o "${DDIR}"/"${VBF_FILE}"
        else
             echo "no zstd installed; exiting"
             exit
@@ -176,7 +184,7 @@ if [[ -f "${SIMDIR}/$VBFNAME" ]]; then
        exit
     fi
 fi
-ls -lh $DDIR/
+ls -lh "$DDIR"/
 
 # check that the uncompressed vbf file exists
 if [[ ! -f "$DDIR/$VBF_FILE" ]]; then
@@ -188,23 +196,41 @@ VBF_FILE="$DDIR/$VBF_FILE"
 
 #######################################
 # option for all steps of the analysis
-MCOPT=" -runnumber=$RUNNUM -sourcetype=2 -epoch $EPOCH -camera=$CFG"
-MCOPT="$MCOPT -reconstructionparameter $ACUTS -sourcefile $VBF_FILE"
-MCOPT="$MCOPT -deadchannelfile $DEAD -donotusedbinfo -calibrationdirectory ${CALDIR}"
-MCOPT="$MCOPT $AMPCORR"
-MCOPT="$MCOPT ${ADD_OPT}"
+read -r -a ADD_OPT_ARR <<< "$ADD_OPT"
+MCOPT=(
+    "-runnumber=$RUNNUM"
+    -sourcetype=2
+    -epoch
+    "$EPOCH"
+    "-camera=$CFG"
+)
+MCOPT+=(
+    -reconstructionparameter
+    "$ACUTS"
+    -sourcefile
+    "$VBF_FILE"
+)
+MCOPT+=(
+    -deadchannelfile
+    "$DEAD"
+    -donotusedbinfo
+    -calibrationdirectory
+    "${CALDIR}"
+)
+MCOPT+=("${AMPCORR[@]}")
+MCOPT+=("${ADD_OPT_ARR[@]}")
 
 # Low gain calibration
 LOWGAINCALIBRATIONFILE=NOFILE
 if [[ ${SIMTYPE:0:4} = "CARE" ]]; then
    if [[ $EDVERSION = "v4"* ]]; then
        if [[ ! -f ${CALDIR}/Calibration/calibrationlist.LowGainForCare.dat ]]; then
-          cp -f $VERITAS_EVNDISP_AUX_DIR/Calibration/calibrationlist.LowGainForCare.dat ${CALDIR}/Calibration/calibrationlist.LowGainForCare.dat
+          cp -f "$VERITAS_EVNDISP_AUX_DIR"/Calibration/calibrationlist.LowGainForCare.dat "${CALDIR}"/Calibration/calibrationlist.LowGainForCare.dat
        fi
        LOWGAINCALIBRATIONFILE=calibrationlist.LowGainForCare.dat
    else
        if [[ ! -f ${CALDIR}/Calibration/calibrationlist.LowGainForCare.${EPOCH:0:2}.dat ]]; then
-          cp -f $VERITAS_EVNDISP_AUX_DIR/Calibration/calibrationlist.LowGainForCare.${EPOCH:0:2}.dat ${CALDIR}/Calibration/calibrationlist.LowGainForCare.${EPOCH:0:2}.dat
+          cp -f "$VERITAS_EVNDISP_AUX_DIR"/Calibration/calibrationlist.LowGainForCare.${EPOCH:0:2}.dat "${CALDIR}"/Calibration/calibrationlist.LowGainForCare.${EPOCH:0:2}.dat
        fi
        LOWGAINCALIBRATIONFILE=calibrationlist.LowGainForCare.${EPOCH:0:2}.dat
    fi
@@ -215,11 +241,11 @@ fi
 # (CARE only, GRISU used external noise file)
 if [[ ${SIMTYPE:0:4} == "CARE" ]]; then
     echo "Calculating pedestals for run $RUNNUM"
-    rm -f $ODIR/$RUNNUM.ped.log
-    PEDOPT="-runmode=1 -calibrationnevents=${PEDNEVENTS}"
-    $EVNDISPSYS/bin/evndisp $MCOPT $PEDOPT &> "$ODIR/$RUNNUM.ped.log"
-    echo "$(inspect_executables)" >> "$ODIR/$RUNNUM.ped.log"
-    if grep -Fq "END OF ANALYSIS, exiting" $ODIR/$RUNNUM.ped.log;
+    rm -f $ODIR/"$RUNNUM".ped.log
+    PEDOPT=("-runmode=1" "-calibrationnevents=${PEDNEVENTS}")
+    "$EVNDISPSYS"/bin/evndisp "${MCOPT[@]}" "${PEDOPT[@]}" &> "$ODIR/$RUNNUM.ped.log"
+    inspect_executables >> "$ODIR/$RUNNUM.ped.log"
+    if grep -Fq "END OF ANALYSIS, exiting" $ODIR/"$RUNNUM".ped.log;
     then
         echo "   successful pedestal analysis"
     else
@@ -231,17 +257,28 @@ fi
 ###############################################
 # calculate tzeros
 echo "Calculating average tzeros for run $RUNNUM"
-TZEROPT="-runmode=7 -calibrationnevents=${TZERONEVENTS} -pedestalnoiselevel=$NOISE "
-TZEROPT="$TZEROPT -lowgainpedestallevel=$LOWPEDLEV -lowgaincalibrationfile ${LOWGAINCALIBRATIONFILE}"
-rm -f $ODIR/$RUNNUM.tzero.log
+TZEROPT=(
+    "-runmode=7"
+    "-calibrationnevents=${TZERONEVENTS}"
+    "-pedestalnoiselevel=$NOISE"
+    "-lowgainpedestallevel=$LOWPEDLEV"
+    -lowgaincalibrationfile
+    "${LOWGAINCALIBRATIONFILE}"
+)
+rm -f $ODIR/"$RUNNUM".tzero.log
 ### eventdisplay GRISU run options
 if [[ ${SIMTYPE:0:5} = "GRISU" ]]; then
-   TZEROPT="$TZEROPT -pedestalfile $NOISEFILE -pedestalseed=$RUNNUM -pedestalDefaultPedestal=$PEDLEV"
+   TZEROPT+=(
+       -pedestalfile
+       "$NOISEFILE"
+       "-pedestalseed=$RUNNUM"
+       "-pedestalDefaultPedestal=$PEDLEV"
+   )
 fi
-echo "$EVNDISPSYS/bin/evndisp $MCOPT $TZEROPT" &> $ODIR/$RUNNUM.tzero.log
-$EVNDISPSYS/bin/evndisp $MCOPT $TZEROPT &>> $ODIR/$RUNNUM.tzero.log
-echo "$(inspect_executables)" &>> "$ODIR/$RUNNUM.tzero.log"
-if grep -Fq "END OF ANALYSIS, exiting" $ODIR/$RUNNUM.tzero.log;
+echo "$EVNDISPSYS/bin/evndisp ${MCOPT[*]} ${TZEROPT[*]}" &> $ODIR/"$RUNNUM".tzero.log
+"$EVNDISPSYS"/bin/evndisp "${MCOPT[@]}" "${TZEROPT[@]}" &>> $ODIR/"$RUNNUM".tzero.log
+inspect_executables &>> "$ODIR/$RUNNUM.tzero.log"
+if grep -Fq "END OF ANALYSIS, exiting" $ODIR/"$RUNNUM".tzero.log;
 then
     echo "   successful tzero analysis"
 else
@@ -255,25 +292,37 @@ fi
 
 #####################
 # general analysis options
-ANAOPT=" -writenomctree -outputfile $DDIR/$ONAME.root"
-ANAOPT="$ANAOPT -lowgaincalibrationfile ${LOWGAINCALIBRATIONFILE} -lowgainpedestallevel=$PEDLEV"
+ANAOPT=(
+    -writenomctree
+    -outputfile
+    "$DDIR/$ONAME.root"
+    -lowgaincalibrationfile
+    "${LOWGAINCALIBRATIONFILE}"
+    "-lowgainpedestallevel=$PEDLEV"
+)
 #
 ######################
 ## options for GRISU (handling of low-gain values)
 if [[ ${SIMTYPE:0:5} == "GRISU" ]]; then
-    ANAOPT="$ANAOPT -simu_hilo_from_simfile -pedestalfile $NOISEFILE -pedestalseed=$RUNNUM -pedestalDefaultPedestal=$PEDLEV"
+    ANAOPT+=(
+        -simu_hilo_from_simfile
+        -pedestalfile
+        "$NOISEFILE"
+        "-pedestalseed=$RUNNUM"
+        "-pedestalDefaultPedestal=$PEDLEV"
+    )
 fi
 #################################################################################
 # run evndisp
 echo "Analysing MC file for run $RUNNUM"
-echo "$EVNDISPSYS/bin/evndisp $MCOPT $ANAOPT" &> $ODIR/$ONAME.log
-$EVNDISPSYS/bin/evndisp $MCOPT $ANAOPT &>> $ODIR/$ONAME.log
-echo "$(inspect_executables)" >> "$ODIR/$ONAME.log"
+echo "$EVNDISPSYS/bin/evndisp ${MCOPT[*]} ${ANAOPT[*]}" &> $ODIR/"$ONAME".log
+"$EVNDISPSYS"/bin/evndisp "${MCOPT[@]}" "${ANAOPT[@]}" &>> $ODIR/"$ONAME".log
+inspect_executables >> "$ODIR/$ONAME.log"
 
 #################################################################################
 # cleanup
 ls -lh "$DDIR"
-cp -r -f -v ${CALDIR}/Calibration ${ODIR}/
+cp -r -f -v "${CALDIR}"/Calibration ${ODIR}/
 rm -f -v "$VBF_FILE"
 
 echo "EVNDISP output root file written to $ODIR/$ONAME.root"
@@ -285,11 +334,11 @@ echo "EVNDISP log file written to $ODIR/$ONAME.log"
 add_log_file()
 {
      # first check if logFile is already included in evndisp file
-     LCON=$($EVNDISPSYS/bin/logFile $1 $DDIR/$ONAME.root | grep "Error: log file object" | wc -l)
+     LCON=$("$EVNDISPSYS"/bin/logFile "$1" "$DDIR"/"$ONAME".root | grep -c "Error: log file object")
      if [[ ${LCON} == 1 ]]; then
          echo "writing log file ${2}"
          if [[ -f ${2} ]]; then
-             $EVNDISPSYS/bin/logFile $1 $DDIR/$ONAME.root ${2}
+             "$EVNDISPSYS"/bin/logFile "$1" "$DDIR"/"$ONAME".root "${2}"
          fi
      else
          echo "log file ${2} already in $DDIR/$ONAME.root"
@@ -306,36 +355,36 @@ add_log_file evndisptzeroLog "$DDIR/$ONAME.tzero.log"
 ### check that log files are filled correctly
 compare_log_file()
 {
-    $EVNDISPSYS/bin/logFile $1 $DDIR/$ONAME.root > ${DDIR}/${1}.log
+    "$EVNDISPSYS"/bin/logFile "$1" "$DDIR"/"$ONAME".root > "${DDIR}"/"${1}".log
     if cmp -s "${2}" "${DDIR}/${1}.log"; then
         echo "FILES ${1} ${2} are the same, removing"
         rm -f "${2}"
     else
-        touch $ODIR/$ONAME.${1}.errorlog
-        echo "Error, ${1} ${2} differ" >> $ODIR/$ONAME.${1}.errorlog
+        touch $ODIR/"$ONAME"."${1}".errorlog
+        echo "Error, ${1} ${2} differ" >> $ODIR/"$ONAME"."${1}".errorlog
     fi
 }
 
-compare_log_file evndispLog $ODIR/$ONAME.log
-if [ -e $ODIR/$ONAME.ped.log ]; then
-    compare_log_file evndisppedLog $ODIR/$ONAME.ped.log
+compare_log_file evndispLog $ODIR/"$ONAME".log
+if [ -e $ODIR/"$ONAME".ped.log ]; then
+    compare_log_file evndisppedLog $ODIR/"$ONAME".ped.log
 fi
-compare_log_file evndisptzeroLog $ODIR/$ONAME.tzero.log
+compare_log_file evndisptzeroLog $ODIR/"$ONAME".tzero.log
 
 ### compress evndisp root file
 compress_file()
 {
     if command -v zstd &>/dev/null; then
-        zstd ${1}
-        zstd --test ${1}.zst
+        zstd "${1}"
+        zstd --test "${1}".zst
     else
         echo "Error: zstd compressing executable not found"
         exit
     fi
 }
 
-compress_file $DDIR/$ONAME.root
-mv -f -v $DDIR/$ONAME.root.zst ${ODIR}/
+compress_file "$DDIR"/"$ONAME".root
+mv -f -v "$DDIR"/"$ONAME".root.zst ${ODIR}/
 
 ### set group permissions
 chmod g+w "$ODIR/$ONAME.root.zst"
diff --git a/scripts/helper_scripts/IRF.lookup_table_combine_sub.sh b/scripts/helper_scripts/IRF.lookup_table_combine_sub.sh
index 020a57b..f63fb61 100755
--- a/scripts/helper_scripts/IRF.lookup_table_combine_sub.sh
+++ b/scripts/helper_scripts/IRF.lookup_table_combine_sub.sh
@@ -1,9 +1,9 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # combine lookup tables
 
 # set observatory environmental variables
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
+# shellcheck source=/dev/null
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
 
@@ -32,7 +32,6 @@ if [ -n "$EVNDISP_APPTAINER" ]; then
     EVNDISPSYS="${EVNDISPSYS/--cleanenv/--cleanenv $APPTAINER_ENV $APPTAINER_MOUNT}"
     echo "APPTAINER SYS: $EVNDISPSYS"
     # path used by EVNDISPSYS needs to be set
-    CALDIR="/opt/ODIR"
 fi
 
 inspect_executables()
@@ -40,7 +39,7 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/evndisp
+        ls -l "${EVNDISPSYS}"/bin/evndisp
     fi
 }
 
@@ -49,13 +48,13 @@ xargs -a "$ODIR/$FLIST" cp -t "$DDIR"
 ls -1 "${DDIR}"/*.root > "$DDIR/$FLIST"
 
 # combine the tables
-$EVNDISPSYS/bin/combineLookupTables "$DDIR/$FLIST" "$DDIR/$OFILE.root" median &> "$ODIR/$OFILE.log"
+"$EVNDISPSYS"/bin/combineLookupTables "$DDIR/$FLIST" "$DDIR/$OFILE.root" median &> "$ODIR/$OFILE.log"
 
 # log files
-echo "$(inspect_executables)" >> "$ODIR/$OFILE.log"
+inspect_executables >> "$ODIR/$OFILE.log"
 cp -v "$ODIR/$OFILE.log" "$DDIR/$OFILE.log"
-$EVNDISPSYS/bin/logFile makeTableCombineLog "$DDIR/$OFILE.root" "$DDIR/$OFILE.log"
-$EVNDISPSYS/bin/logFile makeTableFileList "$DDIR/$OFILE.root" "$DDIR/$FLIST"
+"$EVNDISPSYS"/bin/logFile makeTableCombineLog "$DDIR/$OFILE.root" "$DDIR/$OFILE.log"
+"$EVNDISPSYS"/bin/logFile makeTableFileList "$DDIR/$OFILE.root" "$DDIR/$FLIST"
 
 # cleanup
 mv -f -v "$DDIR/$OFILE.root" "$ODIR/$OFILE.root"
diff --git a/scripts/helper_scripts/IRF.lookup_table_parallel_sub.sh b/scripts/helper_scripts/IRF.lookup_table_parallel_sub.sh
index 9cc900c..ef9867d 100755
--- a/scripts/helper_scripts/IRF.lookup_table_parallel_sub.sh
+++ b/scripts/helper_scripts/IRF.lookup_table_parallel_sub.sh
@@ -1,9 +1,10 @@
 #!/bin/bash
-# shellcheck disable=SC2034,SC2154
+# shellcheck disable=SC2154
 # fill lookup tables
 
 # set observatory environmental variables
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
+# shellcheck source=/dev/null
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
 
@@ -48,7 +49,6 @@ if [ -n "$EVNDISP_APPTAINER" ]; then
     EVNDISPSYS="${EVNDISPSYS/--cleanenv/--cleanenv $APPTAINER_ENV $APPTAINER_MOUNT}"
     echo "APPTAINER SYS: $EVNDISPSYS"
     # path used by EVNDISPSYS needs to be set
-    CALDIR="/opt/ODIR"
 fi
 
 inspect_executables()
@@ -56,14 +56,14 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/mscw_energy
+        ls -l "${EVNDISPSYS}"/bin/mscw_energy
     fi
 }
 
 
 if [ -n "$(find ${INDIR} -name "*[0-9].root" 2>/dev/null)" ]; then
     echo "Copying evndisp root files to ${DDIR}"
-    find ${INDIR} -name "*[0-9].root" -exec cp -v {} ${DDIR} \;
+    find ${INDIR} -name "*[0-9].root" -exec cp -v {} "${DDIR}" \;
 elif [ -n "$(find  ${INDIR} -name "*[0-9].root.zst" 2>/dev/null)" ]; then
     if command -v zstd &>/dev/null; then
         echo "Copying evndisp root.zst files to ${DDIR}"
@@ -71,37 +71,44 @@ elif [ -n "$(find  ${INDIR} -name "*[0-9].root.zst" 2>/dev/null)" ]; then
         for F in $FLIST
         do
             echo "unpacking $F"
-            cp -v -f $F ${DDIR}/
-            ofile=$(basename $F .zst)
-            zstd -d ${DDIR}/${ofile}.zst -o ${DDIR}/${ofile}
+            cp -v -f "$F" "${DDIR}"/
+            ofile=$(basename "$F" .zst)
+            zstd -d "${DDIR}"/"${ofile}".zst -o "${DDIR}"/"${ofile}"
         done
     else
         echo "Error: no zstd installation"
         exit
     fi
 fi
-rm -f "$DDIR/$OFILE.list"
-ls -1 "$DDIR"/*[0-9].root > "$DDIR/$OFILE.list"
+rm -f "$DDIR/$TABFILE.list"
+find "$DDIR" -maxdepth 1 -name "*[0-9].root" > "$DDIR/$TABFILE.list"
 
 # Redo stereo reconstruction with diff cuts on images (versions after v490)
-MOPT=""
+MOPT=()
 if [[ $IRFVERSION != v490* ]]; then
-    MOPT="-redo_stereo_reconstruction -minangle_stereo_reconstruction=10"
-    MOPT="$MOPT -maxloss=0.4 -use_evndisp_selected_images=0"
-    MOPT="$MOPT -maxdist=1.75 -minntubes=5 -minwidth=0.02 -minsize=100"
+    MOPT=(
+        -redo_stereo_reconstruction
+        -minangle_stereo_reconstruction=10
+        -maxloss=0.4
+        -use_evndisp_selected_images=0
+        -maxdist=1.75
+        -minntubes=5
+        -minwidth=0.02
+        -minsize=100
+    )
 fi
 
 echo "Running mscw_energy (table filling)"
 logfile="$ODIR/$TABFILE.log"
-$EVNDISPSYS/bin/mscw_energy -filltables=1 \
+"$EVNDISPSYS"/bin/mscw_energy -filltables=1 \
                             -limitEnergyReconstruction \
                             -write1DHistograms \
-                            -inputfilelist "$DDIR/$OFILE.list" \
+                            -inputfilelist "$DDIR/$TABFILE.list" \
                             -tablefile "${DDIR}/$TABFILE.root" \
-                            -ze=$ZA $MOPT \
+                            -ze=$ZA "${MOPT[@]}" \
                             -arrayrecid=$RECID \
                             -woff=$WOBBLE &> "$logfile"
 
-echo "$(inspect_executables)" >> "$logfile"
-$EVNDISPSYS/bin/logFile makeTableLog "${DDIR}/$TABFILE.root" "$logfile"
+inspect_executables >> "$logfile"
+"$EVNDISPSYS"/bin/logFile makeTableLog "${DDIR}/$TABFILE.root" "$logfile"
 mv -v -f "${DDIR}/$TABFILE.root" "${ODIR}/$TABFILE.root"
diff --git a/scripts/helper_scripts/IRF.mscw_energy_MC_sub.sh b/scripts/helper_scripts/IRF.mscw_energy_MC_sub.sh
index 5f603f8..be9349f 100755
--- a/scripts/helper_scripts/IRF.mscw_energy_MC_sub.sh
+++ b/scripts/helper_scripts/IRF.mscw_energy_MC_sub.sh
@@ -1,10 +1,10 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # Analyse MC files with lookup tables (mscw_energy stage)
 # (optional) Calculate instrument response functions (effective areas) for 4 and 3-telescope combinations
 
 # set observatory environmental variables
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
+# shellcheck source=/dev/null
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
 set -e
@@ -61,7 +61,6 @@ if [ -n "$EVNDISP_APPTAINER" ]; then
     EVNDISPSYS="${EVNDISPSYS/--cleanenv/--cleanenv $APPTAINER_ENV $APPTAINER_MOUNT}"
     echo "APPTAINER SYS: $EVNDISPSYS"
     # path used by EVNDISPSYS needs to be set
-    CALDIR="/opt/ODIR"
     TABFILE="/opt/VERITAS_EVNDISP_AUX_DIR/Tables/$(basename $TABFILE)"
 fi
 
@@ -70,25 +69,40 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/mscw_energy
+        ls -l "${EVNDISPSYS}"/bin/mscw_energy
     fi
 }
 
 # mscw_energy command line options
-MOPT="-noNoTrigger -nomctree -writeReconstructedEventsOnly=1 -arrayrecid=${RECID} -tablefile $TABFILE"
+MOPT=(
+    -noNoTrigger
+    -nomctree
+    -writeReconstructedEventsOnly=1
+    "-arrayrecid=${RECID}"
+    -tablefile
+    "$TABFILE"
+)
 # dispBDT reconstruction
 if [ $DISPBDT -eq 1 ]; then
-    MOPT="$MOPT -redo_stereo_reconstruction"
-    MOPT="$MOPT -tmva_disperror_weight 50"
-    MOPT="$MOPT -minangle_stereo_reconstruction=10."
+    MOPT+=(
+        -redo_stereo_reconstruction
+        -tmva_disperror_weight
+        50
+        -minangle_stereo_reconstruction=10.
+    )
     if [[ $IRFVERSION == v490* ]]; then
-        MOPT="$MOPT -maxloss=0.20"
+        MOPT+=("-maxloss=0.20")
     else
-        MOPT="$MOPT -maxdist=1.75 -minntubes=5 -minwidth=0.02 -minsize=100"
-        MOPT="$MOPT -maxloss=0.40"
-        MOPT="$MOPT -use_evndisp_selected_images=0"
+        MOPT+=(
+            -maxdist=1.75
+            -minntubes=5
+            -minwidth=0.02
+            -minsize=100
+            -maxloss=0.40
+            -use_evndisp_selected_images=0
+        )
     fi
-    # MOPT="$MOPT -maxnevents=1000"
+    # MOPT+=("-maxnevents=1000")
     if [[ ${SIMTYPE} == *"RedHV"* ]]; then
         DISPDIR="${VERITAS_EVNDISP_AUX_DIR}/DispBDTs/${ANATYPE}/${EPOCH}_ATM${ATM}_redHV/"
     elif [[ ${SIMTYPE} == *"UV"* ]]; then
@@ -117,15 +131,23 @@ if [ $DISPBDT -eq 1 ]; then
         fi
     fi
     # unzip XML files into DDIR
-    cp -v -f ${DISPDIR}/*.xml.gz ${DDIR}/
-    gunzip -v ${DDIR}/*xml.gz
-    MOPT="$MOPT -tmva_filename_stereo_reconstruction ${DDIR}/BDTDisp_BDT_"
-    MOPT="$MOPT -tmva_filename_disperror_reconstruction ${DDIR}/BDTDispError_BDT_"
-    MOPT="$MOPT -tmva_filename_dispsign_reconstruction ${DDIR}/BDTDispSign_BDT_"
+    cp -v -f "${DISPDIR}"/*.xml.gz "${DDIR}"/
+    gunzip -v "${DDIR}"/*xml.gz
+    MOPT+=(
+        -tmva_filename_stereo_reconstruction
+        "${DDIR}/BDTDisp_BDT_"
+        -tmva_filename_disperror_reconstruction
+        "${DDIR}/BDTDispError_BDT_"
+        -tmva_filename_dispsign_reconstruction
+        "${DDIR}/BDTDispSign_BDT_"
+    )
     if [[ $IRFVERSION != v490* ]]; then
-        MOPT="$MOPT -tmva_filename_energy_reconstruction ${DDIR}/BDTDispEnergy_BDT_"
+        MOPT+=(
+            -tmva_filename_energy_reconstruction
+            "${DDIR}/BDTDispEnergy_BDT_"
+        )
     fi
-    echo "DISP BDT options: $MOPT"
+    echo "DISP BDT options: ${MOPT[*]}"
 fi
 
 # input evndisp files
@@ -142,9 +164,9 @@ elif [ -n "$(find  "${INDIR}/" -name "*[0-9].root.zst" 2>/dev/null)" ]; then
         for F in $FLIST
         do
             echo "unpacking $F"
-            cp -v -f $F ${DDIR}/
-            ofile=$(basename $F .zst)
-            zstd -d ${DDIR}/${ofile}.zst -o ${DDIR}/${ofile}
+            cp -v -f "$F" "${DDIR}"/
+            ofile=$(basename "$F" .zst)
+            zstd -d "${DDIR}"/"${ofile}".zst -o "${DDIR}"/"${ofile}"
         done
     else
         echo "Error: no zstd installation"
@@ -158,9 +180,9 @@ cat "$DDIR/$OFILE.list"
 echo "Running mscw_energy"
 outputfilename="$DDIR/$OFILE.mscw.root"
 logfile="$OSUBDIR/$OFILE.log"
-$EVNDISPSYS/bin/mscw_energy $MOPT \
+"$EVNDISPSYS"/bin/mscw_energy "${MOPT[@]}" \
     -inputfilelist "$DDIR/$OFILE.list" \
-    -outputfile $outputfilename \
+    -outputfile "$outputfilename" \
     -noise=$NOISE &> $logfile
 
 echo "READING evndisp files from ${INDIR}" >> $logfile
@@ -170,15 +192,15 @@ if [ $DISPBDT -eq 1 ]; then
     echo "Reading DISPBDT XML files from ${DISPDIR}" >> $logfile
 fi
 
-echo "$(inspect_executables)" >> "$logfile"
+inspect_executables >> "$logfile"
 cp -v "$logfile" "$DDIR/$OFILE.log"
-$EVNDISPSYS/bin/logFile mscwTableLog $outputfilename "$DDIR/$OFILE.log"
+"$EVNDISPSYS"/bin/logFile mscwTableLog "$outputfilename" "$DDIR/$OFILE.log"
 
 # cp results file back to data directory and clean up
-outputbasename=$( basename $outputfilename )
+outputbasename=$( basename "$outputfilename" )
 chmod g+w "$logfile"
 if [[ $EFFAREACUTLIST == "NOEFFAREA" ]]; then
-    cp -f -v $outputfilename $OSUBDIR/$outputbasename
+    cp -f -v "$outputfilename" $OSUBDIR/"$outputbasename"
     chmod g+w "$OSUBDIR/$outputbasename"
     exit
 fi
@@ -192,17 +214,17 @@ echo "Effective area generation (cut list: $EFFAREACUTLIST)"
 read_cutlist()
 {
     CUTFILE="${1}"
-    if [[ $CUTFILE == "" ]] || [ ! -f $CUTFILE ]; then
+    if [[ $CUTFILE == "" ]] || [ ! -f "$CUTFILE" ]; then
         echo "Error, cuts list file not found, exiting..." >&2
-        echo $CUTFILE
+        echo "$CUTFILE"
         exit 1
     fi
-    CUTLISTFROMFILE=$(cat $CUTFILE)
+    CUTLISTFROMFILE=$(cat "$CUTFILE")
     CUTLIST=""
     for CUT in "${CUTLISTFROMFILE[@]}"; do
         CUTLIST="${CUTLIST} ANASUM.GammaHadron-Cut-$CUT.dat"
     done
-    echo $CUTLIST
+    echo "$CUTLIST"
 }
 
 # Required for DISP XGB
@@ -230,7 +252,7 @@ check_conda_installation()
 ###############################################
 get_xgb_output_file()
 {
-    XGBOFIL=$(basename $MSCW_FILE .root)
+    XGBOFIL=$(basename "$MSCW_FILE" .root)
     XGBOFIL="${DDIR}/${XGBOFIL}.${XGBVERSION}_ImgSel${1}"
     echo "$XGBOFIL"
 }
@@ -239,6 +261,7 @@ get_xgb_output_file()
 run_xgb()
 {
     check_conda_installation
+# shellcheck source=/dev/null
     source activate base
     conda activate $env_name
     MSCW_FILE="$outputfilename"
@@ -260,7 +283,7 @@ run_xgb()
     DISPDIR="${DISPDIR}/${BIN_ID}/dispdir_bdt"
     echo "DispXGB directory $DISPDIR"
     echo "DispXGB options $XGBVERSION"
-    XGBOFIL=$(get_xgb_output_file $1)
+    XGBOFIL=$(get_xgb_output_file "$1")
     echo "XGB Output file $XGBOFIL"
     echo "DispXGB inputfle $MSCW_FILE"
 
@@ -270,7 +293,7 @@ run_xgb()
         --input-file "$MSCW_FILE" \
         --model-dir "$DISPDIR" \
         --output-file "$XGBOFIL.root" \
-        --image-selection $1 > "$XGBOFIL.log" 2>&1
+        --image-selection "$1" > "$XGBOFIL.log" 2>&1
 
     python --version >> "${XGBOFIL}.log"
     conda list -n $env_name >> "${XGBOFIL}.log"
@@ -300,10 +323,10 @@ for ID in 15 14 13 11 7; do
         fi
         # Check that cuts file exists
         CUTSFILE=${CUTSFILE%%.dat}
-        echo $CUTSFILE
-        CUTS_NAME=$(basename $CUTSFILE)
+        echo "$CUTSFILE"
+        CUTS_NAME=$(basename "$CUTSFILE")
         CUTS_NAME=${CUTS_NAME##ANASUM.GammaHadron-}
-        if [[ "$CUTSFILE" == $(basename $CUTSFILE) ]]; then
+        if [[ "$CUTSFILE" == $(basename "$CUTSFILE") ]]; then
             CUTSFILE="$VERITAS_EVNDISP_AUX_DIR"/GammaHadronCutFiles/$CUTSFILE.dat
         else
             CUTSFILE="$CUTSFILE.dat"
@@ -319,7 +342,7 @@ for ID in 15 14 13 11 7; do
             OSUBDIR="${OSUBDIR}_DISP"
         fi
         echo -e "Output files will be written to:\n $OSUBDIR"
-        mkdir -p $OSUBDIR
+        mkdir -p "$OSUBDIR"
 
         if [[ -n $XGBVERSION ]] && [[ $XGBVERSION != "None" ]]; then
             XGBFILESUFFIX=${XGBVERSION}_ImgSel${ID}
@@ -339,7 +362,7 @@ PARAMFILE="
 * FILLMONTECARLOHISTOS 0
 * ENERGYSPECTRUMINDEX 40 1.5 0.1
 * RERUN_STEREO_RECONSTRUCTION_3TEL $ID
-* CUTFILE $DDIR/$(basename $CUTSFILE)
+* CUTFILE $DDIR/$(basename "$CUTSFILE")
  IGNOREFRACTIONOFEVENTS 0.5
 * SIMULATIONFILE_DATA $outputfilename
 * XGBFILESUFFIX ${XGBFILESUFFIX}"
@@ -351,32 +374,32 @@ PARAMFILE="
         # create makeEffectiveArea parameter file
         EAPARAMS="$EFFAREAFILE-${CUTS_NAME}"
         rm -f "$DDIR/$EAPARAMS.dat"
-        eval "echo \"$PARAMFILE\"" > $DDIR/$EAPARAMS.dat
+        eval "echo \"$PARAMFILE\"" > "$DDIR"/"$EAPARAMS".dat
         echo "Run parameter file:"
-        cat $DDIR/$EAPARAMS.dat
+        cat "$DDIR"/"$EAPARAMS".dat
 
         # calculate effective areas
-        rm -f $OSUBDIR/$OFILE.root
-        $EVNDISPSYS/bin/makeEffectiveArea $DDIR/$EAPARAMS.dat $DDIR/$EAPARAMS.root &> $OSUBDIR/$EAPARAMS.log
+        rm -f "$OSUBDIR"/$OFILE.root
+        "$EVNDISPSYS"/bin/makeEffectiveArea "$DDIR"/"$EAPARAMS".dat "$DDIR"/"$EAPARAMS".root &> "$OSUBDIR"/"$EAPARAMS".log
 
         echo "Filling effAreaLog file into root file: $OSUBDIR/$EAPARAMS.log"
-        echo "$(inspect_executables)" >> "$OSUBDIR/$EAPARAMS.log"
+        inspect_executables >> "$OSUBDIR/$EAPARAMS.log"
         cp "$OSUBDIR/$EAPARAMS.log" "$DDIR/$EAPARAMS.log"
-        $EVNDISPSYS/bin/logFile effAreaLog $DDIR/$EAPARAMS.root $DDIR/$EAPARAMS.log
+        "$EVNDISPSYS"/bin/logFile effAreaLog "$DDIR"/"$EAPARAMS".root "$DDIR"/"$EAPARAMS".log
         echo "Filling mscwTableLog file into root file: $OSUBDIR/$EAPARAMS.log"
-        $EVNDISPSYS/bin/logFile mscwTableLog $DDIR/$EAPARAMS.root "$DDIR/$OFILE.log"
+        "$EVNDISPSYS"/bin/logFile mscwTableLog "$DDIR"/"$EAPARAMS".root "$DDIR/$OFILE.log"
         echo "Trying to fill XGB log file into root file: $OSUBDIR/$EAPARAMS.log"
         if [[ -n $XGBVERSION ]] && [[ $XGBVERSION != "None" ]]; then
             XGBLOGFILE="$(get_xgb_output_file $ID).log"
             if [[ -f "$XGBLOGFILE" ]]; then
-                $EVNDISPSYS/bin/logFile xgbLog $DDIR/$EAPARAMS.root "$XGBLOGFILE"
+                "$EVNDISPSYS"/bin/logFile xgbLog "$DDIR"/"$EAPARAMS".root "$XGBLOGFILE"
             else
                 echo "XGB log file $XGBLOGFILE not found, skipping."
             fi
         fi
-        rm -f $OSUBDIR/$EAPARAMS.log
-        cp -f -v $DDIR/$EAPARAMS.root $OSUBDIR/$EAPARAMS.root
-        chmod -R g+w $OSUBDIR
-        chmod g+w $OSUBDIR/$EAPARAMS.root
+        rm -f "$OSUBDIR"/"$EAPARAMS".log
+        cp -f -v "$DDIR"/"$EAPARAMS".root "$OSUBDIR"/"$EAPARAMS".root
+        chmod -R g+w "$OSUBDIR"
+        chmod g+w "$OSUBDIR"/"$EAPARAMS".root
     done
 done
diff --git a/scripts/helper_scripts/IRF.optimizeTMVAforGammaHadronSeparation_sub.sh b/scripts/helper_scripts/IRF.optimizeTMVAforGammaHadronSeparation_sub.sh
index 2a21da6..02afb5a 100755
--- a/scripts/helper_scripts/IRF.optimizeTMVAforGammaHadronSeparation_sub.sh
+++ b/scripts/helper_scripts/IRF.optimizeTMVAforGammaHadronSeparation_sub.sh
@@ -3,8 +3,9 @@
 # optimize BDTs with TMVA
 #
 
+# shellcheck source=/dev/null
 # set observatory environmental variables
-source $EVNDISPSYS/setObservatory.sh VTS
+source "$EVNDISPSYS"/setObservatory.sh VTS
 
 EFFAREA=EFFFILE
 PREDIR=ODIR
@@ -22,8 +23,8 @@ else
     TEMPDIR="$VERITAS_USER_DATA_DIR/TMPDIR/${CUT}/"
 fi
 echo "Temporary directory: $TEMPDIR"
-mkdir -p $TEMPDIR
-ls -1 ${PREDIR}/${CUT}/*.anasum.root > ${TEMPDIR}/anasum.list
+mkdir -p "$TEMPDIR"
+ls -1 ${PREDIR}/${CUT}/*.anasum.root > "${TEMPDIR}"/anasum.list
 
 OBSTIME="5."
 MINEVENTS="10."
@@ -55,11 +56,11 @@ then
 
     # calculate rates from Crab Nebula and from background rates
     "$EVNDISPSYS"/bin/calculateCrabRateFromMC \
-        ${EFFAREA} \
+        "${EFFAREA}" \
         ${RATEFILE}.root \
         ${DEADTIME} \
         ${TMVAPARFILES} \
-        ${TEMPDIR}/anasum.list \
+        "${TEMPDIR}"/anasum.list \
         > ${RATEFILE}.log
 fi
 
diff --git a/scripts/helper_scripts/IRF.radial_acceptance_sub.sh b/scripts/helper_scripts/IRF.radial_acceptance_sub.sh
index 905795a..0c4e34c 100755
--- a/scripts/helper_scripts/IRF.radial_acceptance_sub.sh
+++ b/scripts/helper_scripts/IRF.radial_acceptance_sub.sh
@@ -1,8 +1,9 @@
 #!/bin/bash
 # generate a radial acceptance file
 
+# shellcheck source=/dev/null
 # set observatory environmental variables
-source $EVNDISPSYS/setObservatory.sh VTS
+source "$EVNDISPSYS"/setObservatory.sh VTS
 
 # parameters replaced by parent script using sed
 RLIST=RUNLIST
@@ -14,8 +15,8 @@ TTA=TELTOANA
 
 # create radial acceptance
 rm -f "$ODIR/$OFILE.log"
-$EVNDISPSYS/bin/makeRadialAcceptance -l $RLIST -c $CUTS -d $DDIR -o $ODIR/$OFILE.root -t $TTA &> $ODIR/$OFILE.log
+"$EVNDISPSYS"/bin/makeRadialAcceptance -l $RLIST -c $CUTS -d $DDIR -o $ODIR/$OFILE.root -t $TTA &> $ODIR/$OFILE.log
 
-$EVNDISPSYS/bin/logFile radAccLOG "$ODIR/$OFILE.root" "$ODIR/$OFILE.log"
+"$EVNDISPSYS"/bin/logFile radAccLOG "$ODIR/$OFILE.root" "$ODIR/$OFILE.log"
 
 exit
diff --git a/scripts/helper_scripts/IRF.trainTMVAforAngularReconstruction_sub.sh b/scripts/helper_scripts/IRF.trainTMVAforAngularReconstruction_sub.sh
index 23e691f..f59c1c6 100755
--- a/scripts/helper_scripts/IRF.trainTMVAforAngularReconstruction_sub.sh
+++ b/scripts/helper_scripts/IRF.trainTMVAforAngularReconstruction_sub.sh
@@ -1,9 +1,9 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # train TMVA (BDTs) for angular reconstruction
 
 # set observatory environmental variables
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
+# shellcheck source=/dev/null
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
 
@@ -37,23 +37,22 @@ if [ -n "$EVNDISP_APPTAINER" ]; then
     EVNDISPSYS="${EVNDISPSYS/--cleanenv/--cleanenv $APPTAINER_ENV $APPTAINER_MOUNT}"
     echo "APPTAINER SYS: $EVNDISPSYS"
     # path used by EVNDISPSYS needs to be set
-    CALDIR="/opt/ODIR"
 fi
 
 # decompress
 NLIST=${ONAME}.list
-echo $NLIST
-for F in $(cat $LLIST)
+echo "$NLIST"
+while IFS= read -r F
 do
-    IDIR=$(dirname $F)
-    OF=${DDIR}/$(basename $IDIR)_$(basename $F)
-    cp -v -f $F ${OF}
-done
-find $DDIR -name "*.root.zst" -exec zstd -f -d {} \;
-ls -1 $DDIR
-ls -1 $DDIR/*.root > ${DDIR}/$NLIST
+    IDIR=$(dirname "$F")
+    OF=${DDIR}/$(basename "$IDIR")_$(basename "$F")
+    cp -v -f "$F" "${OF}"
+done < "$LLIST"
+find "$DDIR" -name "*.root.zst" -exec zstd -f -d {} \;
+ls -1 "$DDIR"
+ls -1 "$DDIR"/*.root > "${DDIR}"/$NLIST
 echo "FILELIST ${DDIR}/$NLIST"
-cat ${DDIR}/$NLIST
+cat "${DDIR}"/$NLIST
 
 ODIR="${ODIR}/${BDT}"
 mkdir -p ${ODIR}
@@ -77,7 +76,7 @@ if [[ $IRFVERSION != v490* ]]; then
     QUALITYCUTS="$(grep 'MVAQUALITYCUTS' $TMVAO | awk '{print $3}')"
     echo "QUALITYCUTS: $QUALITYCUTS"
 
-    $EVNDISPSYS/bin/trainTMVAforAngularReconstruction \
+    "$EVNDISPSYS"/bin/trainTMVAforAngularReconstruction \
         "${DDIR}/${NLIST}" \
         "${DDIR}" \
         "$TRAINTESTFRACTION" \
@@ -88,7 +87,7 @@ if [[ $IRFVERSION != v490* ]]; then
         "${TMVAOPTIONS}" \
         "${EWEIGHT}" > "$ODIR/$ONAME-$BDT-Tel$TELTYPE.log"
 else
-    $EVNDISPSYS/bin/trainTMVAforAngularReconstruction \
+    "$EVNDISPSYS"/bin/trainTMVAforAngularReconstruction \
         "${DDIR}/${NLIST}" \
         "${DDIR}" \
         "$TRAINTESTFRACTION" \
@@ -98,7 +97,7 @@ else
 fi
 
 
-cp -f ${DDIR}/${BDT}_*.root ${ODIR}/
-cp -f ${DDIR}/${BDT}_*.xml ${ODIR}/
+cp -f "${DDIR}"/${BDT}_*.root ${ODIR}/
+cp -f "${DDIR}"/${BDT}_*.xml ${ODIR}/
 # (potentially large training file)
-cp -v ${DDIR}/BDTDisp_${TELTYPE}.root ${ODIR}/
+cp -v "${DDIR}"/BDTDisp_${TELTYPE}.root ${ODIR}/
diff --git a/scripts/helper_scripts/IRF.trainTMVAforGammaHadronSeparation_sub.sh b/scripts/helper_scripts/IRF.trainTMVAforGammaHadronSeparation_sub.sh
index 4c0a4fd..b112fb1 100755
--- a/scripts/helper_scripts/IRF.trainTMVAforGammaHadronSeparation_sub.sh
+++ b/scripts/helper_scripts/IRF.trainTMVAforGammaHadronSeparation_sub.sh
@@ -1,5 +1,4 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # script to train TMVA (BDTs) for gamma/hadron separation
 
 RXPAR=RUNPARAM
@@ -9,6 +8,7 @@ ODIR=OUTPUTDIR
 
 # set observatory environmental variables
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
+# shellcheck source=/dev/null
     source "$EVNDISPSYS"/setObservatory.sh VTS
 fi
 
@@ -28,8 +28,6 @@ if [ -n "$EVNDISP_APPTAINER" ]; then
     EVNDISPSYS="${EVNDISPSYS/--cleanenv/--cleanenv $APPTAINER_ENV $APPTAINER_MOUNT}"
     echo "APPTAINER SYS: $EVNDISPSYS"
     # path used by EVNDISPSYS needs to be set
-    CALDIR="/opt/ODIR"
-
     SIMDIR="/opt/SIMDIR"
     ODIR="/opt/ODIR"
     DDIR="/opt/DDIR"
@@ -48,7 +46,7 @@ inspect_executables()
     if [ -n "$EVNDISP_APPTAINER" ]; then
         apptainer inspect "$EVNDISP_APPTAINER"
     else
-        ls -l ${EVNDISPSYS}/bin/evndisp
+        ls -l "${EVNDISPSYS}"/bin/evndisp
     fi
 }
 
@@ -59,9 +57,9 @@ rm -f "$LDIR/${BASE_RXPAR}_preselect.log"
 rm -f "$LDIR/${BASE_RXPAR}.log"
 "$EVNDISPSYS"/bin/trainTMVAforGammaHadronSeparation "$RXPAR".runparameter.run > "$LDIR/${BASE_RXPAR}.log"
 
-echo "$(inspect_executables)" >> "$LDIR/${BASE_RXPAR}.log"
+inspect_executables >> "$LDIR/${BASE_RXPAR}.log"
 "$EVNDISPSYS"/bin/logFile tmvaLog "$RXPAR".root "$RXPAR".log
 
 # remove unnecessary *.C files
-CDIR=`dirname $RXPAR`
-rm -f -v "$CDIR"/$ONAME*.C
+CDIR=$(dirname "$RXPAR")
+rm -f -v "$CDIR"/"$ONAME"*.C
diff --git a/scripts/helper_scripts/SPANALYSIS.lowgainped_sub.sh b/scripts/helper_scripts/SPANALYSIS.lowgainped_sub.sh
index f06f1c4..c4e7333 100755
--- a/scripts/helper_scripts/SPANALYSIS.lowgainped_sub.sh
+++ b/scripts/helper_scripts/SPANALYSIS.lowgainped_sub.sh
@@ -1,8 +1,9 @@
 #!/bin/bash
 # script to analyse VTS raw files (VBF) with eventdisplay
 
+# shellcheck source=/dev/null
 # set observatory environmental variables
-source $EVNDISPSYS/setObservatory.sh VTS
+source "$EVNDISPSYS"/setObservatory.sh VTS
 
 # parameters replaced by parent script using sed
 RUN=RUNFILE
@@ -19,28 +20,35 @@ else
     TEMPDIR="$VERITAS_USER_DATA_DIR/TMPDIR"
 fi
 echo "Scratch dir: $TEMPDIR"
-mkdir -p $TEMPDIR
+mkdir -p "$TEMPDIR"
 
 LOGDIR="$TEMPDIR"
 
 
 # eventdisplay reconstruction parameter
-ACUTS="EVNDISP.reconstruction.LGCalibration.runparameter"
+ACUTS=("EVNDISP.reconstruction.LGCalibration.runparameter")
 
-OPT=" -calibrationsumwindow=$CALIBRATIONSUMWINDOW -calibrationsumfirst=$CALIBRATIONSUMFIRST -nevents=$NEVENTS -calibrationdirectory $TEMPDIR -teltoana=$TELTOANA "
+OPT=(
+    "-calibrationsumwindow=$CALIBRATIONSUMWINDOW"
+    "-calibrationsumfirst=$CALIBRATIONSUMFIRST"
+    "-nevents=$NEVENTS"
+    -calibrationdirectory
+    "$TEMPDIR"
+    "-teltoana=$TELTOANA"
+)
 
 #########################################
 # pedestal calculation
-rm -f $LOGDIR/$RUN.ped.log
-$EVNDISPSYS/bin/evndisp -runmode=6 -runnumber=$RUN -reconstructionparameter $ACUTS $OPT &> $LOGDIR/$RUN.ped.log
-echo "$EVNDISPSYS/bin/evndisp -runmode=6 -runnumber=$RUN -reconstructionparameter $ACUTS $OPT "
+rm -f "$LOGDIR"/$RUN.ped.log
+"$EVNDISPSYS"/bin/evndisp -runmode=6 -runnumber="$RUN" -reconstructionparameter "${ACUTS[@]}" "${OPT[@]}" &> "$LOGDIR"/$RUN.ped.log
+echo "$EVNDISPSYS/bin/evndisp -runmode=6 -runnumber=$RUN -reconstructionparameter ${ACUTS[*]} ${OPT[*]}"
 
 for ((i=1; i<5; i++))
 do
 	mkdir -p $CALDIR/Calibration/Tel_$i/
-	mv $TEMPDIR/Calibration/Tel_$i/$RUN.lped $CALDIR/Calibration/Tel_$i/
-	mv $TEMPDIR/Calibration/Tel_$i/$RUN.lped.root $CALDIR/Calibration/Tel_$i/
-	mv $LOGDIR/$RUN.ped.log $CALDIR/
+	mv "$TEMPDIR"/Calibration/Tel_$i/$RUN.lped $CALDIR/Calibration/Tel_$i/
+	mv "$TEMPDIR"/Calibration/Tel_$i/$RUN.lped.root $CALDIR/Calibration/Tel_$i/
+	mv "$LOGDIR"/$RUN.ped.log $CALDIR/
 done
 
 exit
diff --git a/scripts/helper_scripts/SPANALYSIS.make_DST_sub.sh b/scripts/helper_scripts/SPANALYSIS.make_DST_sub.sh
index 15be9be..b0e2c0d 100755
--- a/scripts/helper_scripts/SPANALYSIS.make_DST_sub.sh
+++ b/scripts/helper_scripts/SPANALYSIS.make_DST_sub.sh
@@ -1,13 +1,14 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # script to make DSTs
 
 # set observatory environmental variables
-source $EVNDISPSYS/setObservatory.sh VTS
+# shellcheck source=/dev/null
+source "$EVNDISPSYS"/setObservatory.sh VTS
 
 # parameters replaced by parent script using sed
 RUN=RUNFILE
 PED=PEDESTALS
+# shellcheck disable=SC2034  # template placeholder, replaced by sed before job submission
 SUMW=SUMWINDOW
 LMULT=LLLOWGAIN
 
@@ -18,7 +19,7 @@ else
     TEMPDIR="$VERITAS_USER_DATA_DIR/TMPDIR"
 fi
 echo "Temporary directory: $TEMPDIR"
-mkdir -p $TEMPDIR
+mkdir -p "$TEMPDIR"
 
 # output data files are written to this directory
 ODIR=OUTPUTDIR
@@ -29,17 +30,17 @@ LOGDIR="$ODIR"
 mkdir -p $LOGDIR
 
 # eventdisplay reconstruction parameter
-ACUTS=RRRRPFILE
+ACUTS=("RRRRPFILE")
 
 #########################################
 # pedestal and tzero calculation. No tzeros needed for lmult.
 if [[ $PED == "1" ]]; then
     rm -f $LOGDIR/$RUN.ped.log
-    $EVNDISPSYS/bin/evndisp -runnumber=$RUN -runmode=1 &> $LOGDIR/$RUN.ped.log
+    "$EVNDISPSYS"/bin/evndisp -runnumber=$RUN -runmode=1 &> $LOGDIR/$RUN.ped.log
 
     if [[ $LMULT == "0" ]] ; then
 	rm -f $LOGDIR/$RUN.tzero.log
-    	$EVNDISPSYS/bin/evndisp -runnumber=$RUN -runmode=7 -nocalibnoproblem &> $LOGDIR/$RUN.tzero.log
+	"$EVNDISPSYS"/bin/evndisp -runnumber=$RUN -runmode=7 -nocalibnoproblem &> $LOGDIR/$RUN.tzero.log
     fi
 fi
 
@@ -47,18 +48,18 @@ fi
 #########################################
 # Other options. hilo runs should have all events analysed.
 if [[ $LMULT == "0" ]] ; then
-	OPT=" -nevents=5000 "
+    OPT=("-nevents=5000")
 else
-	OPT=" -lowgaincalibrationfile calibrationlist.LowGain.CALIB.dat "
+    OPT=(-lowgaincalibrationfile calibrationlist.LowGain.CALIB.dat)
 fi
 
 #########################################
 # run eventdisplay
 rm -f $LOGDIR/$RUN.log
-$EVNDISPSYS/bin/evndisp -runnumber=$RUN -runmode=4 -nocalibnoproblem $OPT -reconstructionparameter $ACUTS -dstfile $TEMPDIR/$RUN.DST.root &> $LOGDIR/$RUN.DST.log
+"$EVNDISPSYS"/bin/evndisp -runnumber="$RUN" -runmode=4 -nocalibnoproblem "${OPT[@]}" -reconstructionparameter "${ACUTS[@]}" -dstfile "$TEMPDIR"/$RUN.DST.root &> $LOGDIR/$RUN.DST.log
 
 # move data file from temp dir to data dir
-cp -f -v $TEMPDIR/$RUN.DST.root $ODIR/$RUN.DST.root
-rm -f $TEMPDIR/$RUN.DST.root
+cp -f -v "$TEMPDIR"/$RUN.DST.root $ODIR/$RUN.DST.root
+rm -f "$TEMPDIR"/$RUN.DST.root
 
 exit
diff --git a/scripts/helper_scripts/UTILITY.check_root_file_closed.sh b/scripts/helper_scripts/UTILITY.check_root_file_closed.sh
index 9650c29..05af647 100755
--- a/scripts/helper_scripts/UTILITY.check_root_file_closed.sh
+++ b/scripts/helper_scripts/UTILITY.check_root_file_closed.sh
@@ -6,9 +6,8 @@ if [ "$1" == "" ]; then
     echo "Usage: $0 root_file_to_check_if_closed.root"
 fi
 
-filename_to_check=$(readlink -f $1)
+filename_to_check=$(readlink -f "$1")
 #echo $filename_to_check
-root -b -l -q -e "$EVNDISPSYS/macros/checkCorrupted.C(\"$filename_to_check\")" >/dev/null 2>&1
-if [ $? -ne 0 ]; then
+if ! root -b -l -q -e "$EVNDISPSYS/macros/checkCorrupted.C(\"$filename_to_check\")" >/dev/null 2>&1; then
     exit 1
 fi
diff --git a/scripts/helper_scripts/UTILITY.condorSubmission.sh b/scripts/helper_scripts/UTILITY.condorSubmission.sh
index 7e95a93..43391e7 100755
--- a/scripts/helper_scripts/UTILITY.condorSubmission.sh
+++ b/scripts/helper_scripts/UTILITY.condorSubmission.sh
@@ -15,7 +15,7 @@ SUBFIL=${SUBSCRIPT}.condor
 
 [[ -f "$SUBFIL" ]] && rm -f "$SUBFIL".
 
-cat > ${SUBFIL} <<EOL
+cat > "${SUBFIL}" <<EOL
 Executable = ${SUBSCRIPT}
 Output = ${SUBSCRIPT}.\$(Cluster)_\$(Process).output
 Error = ${SUBSCRIPT}.\$(Cluster)_\$(Process).error
diff --git a/scripts/helper_scripts/UTILITY.readSubmissionCommand.sh b/scripts/helper_scripts/UTILITY.readSubmissionCommand.sh
index b668392..61a6031 100755
--- a/scripts/helper_scripts/UTILITY.readSubmissionCommand.sh
+++ b/scripts/helper_scripts/UTILITY.readSubmissionCommand.sh
@@ -29,17 +29,17 @@ fi
 
 # Use submission command with * in front; if multiple commands have an *,
 # the command that is farthest down in the file will be used
-while read STAR LINE; do
+while read -r STAR LINE; do
     if [[ $STAR = "*" ]]; then
         CMD=$LINE
     fi
-done < $CMDFILE
+done < "$CMDFILE"
 
 if [[ -z "$CMD" ]]; then
     echo "ERROR! No submission command is selected in $CMDFILE."
     exit 1
 else
-    echo $CMD
+    echo "$CMD"
 fi
 
 exit
diff --git a/scripts/helper_scripts/UTILITY.script_init.sh b/scripts/helper_scripts/UTILITY.script_init.sh
index f9789de..06974f9 100755
--- a/scripts/helper_scripts/UTILITY.script_init.sh
+++ b/scripts/helper_scripts/UTILITY.script_init.sh
@@ -23,8 +23,9 @@ if [[ -z $VERITAS_USER_LOG_DIR ]]; then
     exit 1
 fi
 
+# shellcheck source=/dev/null
 # set the right observatory (environmental variables)
-source $EVNDISPSYS/setObservatory.sh VTS -q
+source "$EVNDISPSYS"/setObservatory.sh VTS -q
 
 # return 0 if successful
 exit 0
diff --git a/scripts/helper_scripts/submit_scripts_to_htcondor.sh b/scripts/helper_scripts/submit_scripts_to_htcondor.sh
index 6b1a632..4c119c4 100755
--- a/scripts/helper_scripts/submit_scripts_to_htcondor.sh
+++ b/scripts/helper_scripts/submit_scripts_to_htcondor.sh
@@ -24,33 +24,37 @@ PRIORITY="${3:-1}"
 echo "Writing HTCondor job submission file ${SUBMITF} (job priority $PRIORITY) for ${JDIR}"
 if find "${JDIR}" -name "*.condor" -print -quit | grep -q .; then
     SUBMITF=${1}/submit.txt
-    rm -f ${SUBMITF}
-    touch ${SUBMITF}
+    rm -f "${SUBMITF}"
+    touch "${SUBMITF}"
 
-    mkdir -p ${JDIR}/log
-    mkdir -p ${JDIR}/output
-    mkdir -p ${JDIR}/error
+    mkdir -p "${JDIR}"/log
+    mkdir -p "${JDIR}"/output
+    mkdir -p "${JDIR}"/error
 
-    echo "executable = \$(file)" >>  ${SUBMITF}
-    echo "log = log/\$(file).log" >>  ${SUBMITF}
-    echo "output = output/\$(file).output" >>  ${SUBMITF}
-    echo "error = error/\$(file).error" >>  ${SUBMITF}
+    {
+        echo "executable = \$(file)"
+        echo "log = log/\$(file).log"
+        echo "output = output/\$(file).output"
+        echo "error = error/\$(file).error"
+    } >> "${SUBMITF}"
 
     # assume that all condor files have similar requests
-    CONDORFILE=$(find ${JDIR} -name "*.condor" | head -n 1)
-    echo "$(grep -h request_memory $CONDORFILE)"  >>  ${SUBMITF}
-    echo "$(grep -h request_disk $CONDORFILE)"  >>  ${SUBMITF}
-    echo "getenv = True" >>  ${SUBMITF}
-    echo "max_materialize = 1800" >>  ${SUBMITF}
-#    echo "request_cpus = 8" >>  ${SUBMITF}
-    echo "priority = $PRIORITY"  >> ${SUBMITF}
-    echo "queue file matching files *.sh" >> ${SUBMITF}
+    CONDORFILE=$(find "${JDIR}" -name "*.condor" | head -n 1)
+    {
+        grep -h request_memory "$CONDORFILE"
+        grep -h request_disk "$CONDORFILE"
+        echo "getenv = True"
+        echo "max_materialize = 1800"
+#        echo "request_cpus = 8"
+        echo "priority = $PRIORITY"
+        echo "queue file matching files *.sh"
+    } >> "${SUBMITF}"
 
     PDIR=$(pwd)
     if [ "${2}" = "submit" ]; then
-        cd ${JDIR}
+        cd "${JDIR}"
         condor_submit submit.txt requirements='OpSysAndVer=="AlmaLinux9"'
-        cd ${PDIR}
+        cd "${PDIR}"
     fi
 else
     echo "Error: no condor files found in ${JDIR}"
diff --git a/scripts/preprocessing/archive_error_files.sh b/scripts/preprocessing/archive_error_files.sh
index 1a4aab4..2b32e56 100755
--- a/scripts/preprocessing/archive_error_files.sh
+++ b/scripts/preprocessing/archive_error_files.sh
@@ -1,5 +1,4 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # Move Eventdisplay data products from all stages
 # into an runs_with_issues directory.
 # runs are given in a run list
@@ -16,7 +15,7 @@ fi
 
 RUNLIST=${1}
 
-EDVERSION=`$EVNDISPSYS/bin/evndisp --version | tr -d .`
+EDVERSION=$("$EVNDISPSYS"/bin/evndisp --version | tr -d .)
 # list of data products
 DP="evndisp mscw anasum_moderate2tel"
 # archive directory
@@ -25,7 +24,7 @@ do
     DDIR=${VERITAS_DATA_DIR}/processed_data_${EDVERSION}/${VERITAS_ANALYSIS_TYPE:0:2}/runs_with_issues/${D}
     for N in 3 4 5 6 7 8 9 10 11
     do
-        mkdir -p -v ${DDIR}/$N
+        mkdir -p -v "${DDIR}"/$N
     done
 done
 
@@ -37,10 +36,10 @@ get_suffix()
     else
         SRUN=${RRUN:0:2}
     fi
-    echo ${SRUN}
+    echo "${SRUN}"
 }
 
-FF=$(cat ${1})
+FF=$(cat "$RUNLIST")
 
 for D in $DP
 do
diff --git a/scripts/preprocessing/check_dl3_number_of_files_per_cut.sh b/scripts/preprocessing/check_dl3_number_of_files_per_cut.sh
index dbb42b1..3f77e2e 100755
--- a/scripts/preprocessing/check_dl3_number_of_files_per_cut.sh
+++ b/scripts/preprocessing/check_dl3_number_of_files_per_cut.sh
@@ -10,7 +10,7 @@ Check number of DL3 fits and log files for all cuts and analysis types.
 "
 fi
 
-NFIL=$(find ${1}/point-like -name "*.fits.gz" | wc -l)
+NFIL=$(find "${1}"/point-like -name "*.fits.gz" | wc -l)
 
 if [[ ${VERITAS_ANALYSIS_TYPE:0:2} == "AP" ]]; then
     CUTS="moderate2tel soft2tel hard2tel hard3tel"
@@ -23,8 +23,8 @@ TYPES="dl3_pointlike-all dl3_pointlike dl3_fullenclosure-all-events dl3_fullencl
 for T in $TYPES; do
     for C in $CUTS; do
         echo "Checking $T $C in ${1}/${T}_${C}"
-        NFIL=$(find ${1}/${T}_${C} -name "*.fits.gz" | wc -l)
-        NLOG=$(find ${1}/${T}_${C} -name "*.log" | wc -l)
+        NFIL=$(find "${1}"/"${T}"_"${C}" -name "*.fits.gz" | wc -l)
+        NLOG=$(find "${1}"/"${T}"_"${C}" -name "*.log" | wc -l)
         echo "Number of files: $NFIL $NLOG"
     done
 done
diff --git a/scripts/preprocessing/check_epochs_for_3tel_irfs.sh b/scripts/preprocessing/check_epochs_for_3tel_irfs.sh
index da6abb3..12a9a0c 100755
--- a/scripts/preprocessing/check_epochs_for_3tel_irfs.sh
+++ b/scripts/preprocessing/check_epochs_for_3tel_irfs.sh
@@ -11,7 +11,7 @@ exit
 fi
 
 RUNLIST="${1}"
-RUNS=$(cat $RUNLIST)
+RUNS=$(cat "$RUNLIST")
 
 DDIR="$VERITAS_PREPROCESSED_DATA_DIR/${VERITAS_ANALYSIS_TYPE:0:2}/mscw/"
 
@@ -32,14 +32,14 @@ getNumberedDirectory()
     else
         NDIR="${IDIR}/${TRUN:0:2}/"
     fi
-    echo ${NDIR}
+    echo "${NDIR}"
 }
 
 for R in $RUNS; do
-    LOGDIR=$(getNumberedDirectory $R ${DDIR})
+    LOGDIR=$(getNumberedDirectory "$R" "${DDIR}")
     LOGFIL="${LOGDIR}/${R}.mscw.log"
     if [[ -e $LOGFIL ]]; then
-        TELSTRING=$(grep "Mean pedvar per telescope" ${LOGFIL})
+        TELSTRING=$(grep "Mean pedvar per telescope" "${LOGFIL}")
         mapfile -t pedvars < <(echo "$TELSTRING" | awk '{for(i=5;i<=NF;i++) print $i}')
         T="T"
         for i in "${!pedvars[@]}"; do
@@ -49,9 +49,9 @@ for R in $RUNS; do
             fi
         done
         if [[ $T != "T1234" ]]; then
-            EPOCHSTRING=$(grep "Evaluating instrument" ${LOGFIL})
+            EPOCHSTRING=$(grep "Evaluating instrument" "${LOGFIL}")
             EPOCH=$(echo "$EPOCHSTRING" | sed -n 's/.*is: \([^)]*\)).*/\1/p')
-            ATMOSTRING=$(grep "Evaluating atmosphere ID" ${LOGFIL})
+            ATMOSTRING=$(grep "Evaluating atmosphere ID" "${LOGFIL}")
             ATMOID=$(echo "$ATMOSTRING" | sed -n 's/.*is: \([0-9]*\)).*/\1/p')
             if [[ $T == "T123" ]]; then
                 ID=5
diff --git a/scripts/preprocessing/check_evndisp_mscw_processing.sh b/scripts/preprocessing/check_evndisp_mscw_processing.sh
index 8b10dcb..d892f66 100755
--- a/scripts/preprocessing/check_evndisp_mscw_processing.sh
+++ b/scripts/preprocessing/check_evndisp_mscw_processing.sh
@@ -12,9 +12,9 @@ echo "
 exit
 fi
 
-FF=$(cat ${1})
+FF=$(cat "${1}")
 DTYPE=${2}
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFMINORVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFMINORVERSION)
 
 file_on_disk()
 {
diff --git a/scripts/preprocessing/pack_data_files.sh b/scripts/preprocessing/pack_data_files.sh
index 22efa92..f685228 100755
--- a/scripts/preprocessing/pack_data_files.sh
+++ b/scripts/preprocessing/pack_data_files.sh
@@ -25,11 +25,11 @@ fi
 DATATYPE=${1}
 RUNLIST=${2}
 
-VERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFMINORVERSION)
-RUNS=$(cat $RUNLIST)
+VERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFMINORVERSION)
+RUNS=$(cat "$RUNLIST")
 
 TMPDATADIR="$VERITAS_USER_DATA_DIR/tmp_packing/${3}/${DATATYPE}"
-mkdir -p ${TMPDATADIR}
+mkdir -p "${TMPDATADIR}"
 
 get_suffix()
 {
@@ -39,13 +39,13 @@ get_suffix()
     else
         SRUN=${RRUN:0:2}
     fi
-    echo ${SRUN}
+    echo "${SRUN}"
 }
 
 get_file_name()
 {
     RRUN=${1}
-    SRUN=$(get_suffix ${RRUN})
+    SRUN=$(get_suffix "${RRUN}")
     if [[ $DATATYPE == "evndisp" ]]; then
         echo "$VERITAS_DATA_DIR/processed_data_${VERSION}/${ANATYPE}/${DATATYPE}/${SRUN}/${RRUN}.root"
     elif [[ $DATATYPE == "mscw" ]]; then
@@ -57,24 +57,24 @@ get_file_name()
 
 for R in $RUNS
 do
-    F=$(get_file_name $R)
+    F=$(get_file_name "$R")
     if [[ ! -f ${F} ]] || [[ -z ${F} ]]; then
         echo "RUN ${R} not processed for ${DATATYPE} (${ANATYPE})"
         continue
     fi
     echo "FOUND ${F}"
-    SRUN=$(get_suffix ${R})
-    mkdir -p ${TMPDATADIR}/${SRUN}
-    cp -f -v ${F} ${TMPDATADIR}/${SRUN}
+    SRUN=$(get_suffix "${R}")
+    mkdir -p "${TMPDATADIR}"/"${SRUN}"
+    cp -f -v "${F}" "${TMPDATADIR}"/"${SRUN}"
 done
 
-DTOPACK=$(find ${TMPDATADIR}  -mindepth 1 -name "[0-9]*" -type d)
+DTOPACK=$(find "${TMPDATADIR}"  -mindepth 1 -name "[0-9]*" -type d)
 for D in ${DTOPACK}
 do
     echo "Packing $D"
     # removing leading directory path
     RMDATADIR="${TMPDATADIR/\/}"
     RMDATADIR="${RMDATADIR/$DATATYPE/}"
-    tar --transform "s|^$RMDATADIR||" -cvzf ${D}.${DATATYPE}.tar.gz ${D}
+    tar --transform "s|^$RMDATADIR||" -cvzf "${D}"."${DATATYPE}".tar.gz "${D}"
 done
 echo "TAR FILE: ${D}.${DATATYPE}.tar.gz"
diff --git a/scripts/preprocessing/pack_log_files.sh b/scripts/preprocessing/pack_log_files.sh
index 58a0710..9b3c8cb 100755
--- a/scripts/preprocessing/pack_log_files.sh
+++ b/scripts/preprocessing/pack_log_files.sh
@@ -24,7 +24,7 @@ DDIRS=$(cat "$DLIST")
 cd "${PDIR}" || exit
 
 for DIR in $DDIRS; do
-    echo $DIR
-    rm -f logs_${DIR}.tar.gz
-    find ${DIR} -type f -name "*.log" -exec tar -rf logs_${DIR}.tar.gz {} +
+    echo "$DIR"
+    rm -f logs_"${DIR}".tar.gz
+    find "${DIR}" -type f -name "*.log" -exec tar -rf logs_"${DIR}".tar.gz {} +
 done
diff --git a/scripts/preprocessing/prepare_runlist_after_dqm.sh b/scripts/preprocessing/prepare_runlist_after_dqm.sh
index 950e4aa..1437031 100755
--- a/scripts/preprocessing/prepare_runlist_after_dqm.sh
+++ b/scripts/preprocessing/prepare_runlist_after_dqm.sh
@@ -30,7 +30,7 @@ DBTEXTDIRECTORY="$VERITAS_PREPROCESSED_DATA_DIR/../DBTEXT"
 
 # List of broken runs
 # (not caught with the logic below)
-BROKENRUNS=$(cut -d ' ' -f 1 ${2})
+BROKENRUNS=$(cut -d ' ' -f 1 "${2}")
 
 get_db_text_tar_file()
 {
@@ -94,9 +94,9 @@ fill_run()
 
 fill_timemask()
 {
-    TMASK_1=$(echo $2 | cut -d '/' -f 1)
+    TMASK_1=$(echo "$2" | cut -d '/' -f 1)
     TMASK_1=$(printf "%.0f" "$TMASK_1")
-    TMASK_2=$(echo $2 | cut -d '/' -f 2)
+    TMASK_2=$(echo "$2" | cut -d '/' -f 2)
     TMASK_2=$(printf "%.0f" "$TMASK_2")
     TMASK="* $1 $TMASK_1 $((TMASK_2 - TMASK_1)) 0"
     echo "$TMASK" >> timemask.dat
@@ -105,7 +105,7 @@ fill_timemask()
 
 prepare_output_files
 
-RUNS=$(cat $RUNLIST)
+RUNS=$(cat "$RUNLIST")
 
 for RF in $RUNS
 do
@@ -121,7 +121,7 @@ do
         echo "   RUN $R broken (BROKENCUT APPLIED)"
         continue
     fi
-    DBTEXTFILE=$(get_db_text_tar_file ${R})
+    DBTEXTFILE=$(get_db_text_tar_file "${R}")
     # Target file
     TARGETFILE="${R}/${R}.target"
     # DQM File
@@ -131,14 +131,14 @@ do
     if [[ -e ${DBTEXTFILE} ]]; then
         #####
         # Check target
-        if [[ -z $(tar -tzf ${DBTEXTFILE} | grep "${TARGETFILE}") ]]; then
+        if [[ -z $(tar -tzf "${DBTEXTFILE}" | grep "${TARGETFILE}") ]]; then
             echo "   RUN $R no target file ${TARGETFILE} found (NOTARGETFILE CUT APPLIED)"
-            echo ${R} >> runlist_NOTARGETFILE.dat
+            echo "${R}" >> runlist_NOTARGETFILE.dat
             continue
         fi
         # TARGET string
-        TARGETSTRING=$(tar -axf ${DBTEXTFILE} ${TARGETFILE} -O)
-        echo $TARGETSTRING
+        TARGETSTRING=$(tar -axf "${DBTEXTFILE}" "${TARGETFILE}" -O)
+        echo "$TARGETSTRING"
         # skip targets DARK...
         RTARGET=$(echo "${TARGETSTRING}" | cut -d '|' -f 1 | grep -v source_id)
         echo "   RUN $R  $RTARGET"
@@ -153,21 +153,21 @@ do
         fi
         # skip laser and flasher runs
         if [[ $RTARGET == "laser" ]] || [[ $RTARGET == "flasher" ]]; then
-            echo "   RUN $R $TARGET target (FLASHER CUT APPLIED)"
+            echo "   RUN $R $RTARGET target (FLASHER CUT APPLIED)"
             continue
         fi
-        if [[ -z $(tar -tzf ${DBTEXTFILE} | grep "${DQMFILE}") ]]; then
+        if [[ -z $(tar -tzf "${DBTEXTFILE}" | grep "${DQMFILE}") ]]; then
             echo "   RUN $R no DQM file ${DQMFILE} found (NODQMFILE CUT APPLIED)"
-            echo ${R} >> runlist_NODQM.dat
+            echo "${R}" >> runlist_NODQM.dat
             continue
         fi
         #####
         # Check DQM
         # DQM string
-        DQMSTRING=$(tar -axf ${DBTEXTFILE} ${DQMFILE} -O)
-        echo $DQMSTRING
+        DQMSTRING=$(tar -axf "${DBTEXTFILE}" "${DQMFILE}" -O)
+        echo "$DQMSTRING"
         # data category
-        RCAT=$(echo "${DQMSTRING}" | cut -d '|' -f 2 ${RDQM} | grep -v data_category)
+        RCAT=$(echo "${DQMSTRING}" | cut -d '|' -f 2 "${RDQM}" | grep -v data_category)
         # (especially early runs do not have a science category)
         if [[ ${RCAT} != "science" ]] \
             && [[ ${RCAT} != "reducedhv" ]] \
@@ -177,23 +177,23 @@ do
             continue
         fi
         # DQM status
-        RSTATUS=$(echo "${DQMSTRING}" | cut -d '|' -f 3 ${RDQM} | grep -v status)
+        RSTATUS=$(echo "${DQMSTRING}" | cut -d '|' -f 3 "${RDQM}" | grep -v status)
         if [[ ${RSTATUS} == "do_not_use" ]] || [[ ${RSTATUS} == "NULL" ]]; then
             # early V4 runs without DQM
             if [[ ${RSTATUS} == "do_not_use" ]] || [[ $R -gt 46642 ]]; then
                 echo "   RUN $R $RSTATUS (STATUS CUT APPLIED)"
                 if [[ ${RSTATUS} == "NULL" ]] && [[ ${RCAT} != "NULL" ]]; then
-                    echo $R >> runlist_NULL.dat
+                    echo "$R" >> runlist_NULL.dat
                 fi
                 continue
             fi
         fi
-        INFOSTRING=$(tar -axf ${DBTEXTFILE} ${INFOFILE} -O)
-        echo $INFOSTRING
+        INFOSTRING=$(tar -axf "${DBTEXTFILE}" "${INFOFILE}" -O)
+        echo "$INFOSTRING"
         # usable duration
-        RUSABLE=$(echo "${DQMSTRING}" | cut -d '|' -f 6 ${RDQM} | grep -v usable_duration)
+        RUSABLE=$(echo "${DQMSTRING}" | cut -d '|' -f 6 "${RDQM}" | grep -v usable_duration)
         if [[ $RUSABLE != "NULL" ]]; then
-            RTUSABLE=$(echo $RUSABLE | awk 'NR==1 {split($1, arr, "[:]"); print arr[2]}')
+            RTUSABLE=$(echo "$RUSABLE" | awk 'NR==1 {split($1, arr, "[:]"); print arr[2]}')
             if [[ $((10#$RTUSABLE)) -lt 2 ]]; then
                 echo "   RUN $R $RSTATUS $RTUSABLE (TIME CUT APPLIED; $RUSABLE)"
                 continue
@@ -204,8 +204,8 @@ do
             continue
         fi
         # data duration frum run info
-        RDATAT1=$(echo "${INFOSTRING}" | cut -d '|' -f 7 ${RDQM} | grep -v data_start_time)
-        RDATAT2=$(echo "${INFOSTRING}" | cut -d '|' -f 8 ${RDQM} | grep -v data_end_time)
+        RDATAT1=$(echo "${INFOSTRING}" | cut -d '|' -f 7 "${RDQM}" | grep -v data_start_time)
+        RDATAT2=$(echo "${INFOSTRING}" | cut -d '|' -f 8 "${RDQM}" | grep -v data_end_time)
         echo "  RUN $R $RDATAT1 $RDATAT2"
         RDATAT1=$(date -u -d "$RDATAT1" +%s)
         RDATAT2=$(date -u -d "$RDATAT2" +%s)
@@ -216,12 +216,12 @@ do
             continue
         fi
         # time mask
-        RCUTMASK=$(echo "${DQMSTRING}" | cut -d '|' -f 7 ${RDQM} | grep -v time_cut_mask)
+        RCUTMASK=$(echo "${DQMSTRING}" | cut -d '|' -f 7 "${RDQM}" | grep -v time_cut_mask)
         if [[ $RCUTMASK != "NULL" ]]; then
             IFS=','
             for TCUT in $RCUTMASK
             do
-                fill_timemask $R $TCUT
+                fill_timemask "$R" "$TCUT"
             done
         fi
     else
@@ -229,7 +229,7 @@ do
         RCUTMASK="NULL"
     fi
     echo "   $R $RSTATUS $RUSABLE $RCUTMASK"
-    fill_run $R $RCAT
+    fill_run "$R" "$RCAT"
 done
 
 sort_output_files
diff --git a/scripts/preprocessing/prepro_check_and_clean_files.sh b/scripts/preprocessing/prepro_check_and_clean_files.sh
index 5e43ad2..3fe0a73 100755
--- a/scripts/preprocessing/prepro_check_and_clean_files.sh
+++ b/scripts/preprocessing/prepro_check_and_clean_files.sh
@@ -34,7 +34,7 @@ move_list()
 
 
 # find all runs with errors and move them
-FLIST=$(grep -irl "error" $FTYPE/*.log)
+FLIST=$(grep -irl "error" "$FTYPE"/*.log)
 if [[ -n $FLIST ]]; then
     file_count=$(echo "$FLIST" | wc -w)
     if [[ ! -z $file_count ]]; then
@@ -43,7 +43,7 @@ if [[ -n $FLIST ]]; then
     move_list error "$FLIST"
 fi
 # find all runs with segmentation faults
-FLIST=$(grep -rl "segmentation" $FTYPE/*.log)
+FLIST=$(grep -rl "segmentation" "$FTYPE"/*.log)
 if [[ -n $FLIST ]]; then
     file_count=$(echo "$FLIST" | wc -w)
     if [[ ! -z $file_count ]]; then
@@ -52,7 +52,7 @@ if [[ -n $FLIST ]]; then
     move_list error "$FLIST"
 fi
 # find all runs without errors and remove them from error directory
-FLIST=$(grep -iL "error" $FTYPE/*.log)
+FLIST=$(grep -iL "error" "$FTYPE"/*.log)
 if [[ -n $FLIST ]]; then
     file_count=$(echo "$FLIST" | wc -w)
     if [[ ! -z $file_count ]]; then
@@ -64,7 +64,7 @@ if [[ -n $FLIST ]]; then
 fi
 
 echo "Aux data (and NOTFOUND)"
-NAUX=$(ls -1 "$FTYPE"/*.NOTFOUND 2>/dev/null | wc -l)
+NAUX=$(find "$FTYPE" -maxdepth 1 -name "*.NOTFOUND" 2>/dev/null | wc -l)
 if [[ $NAUX -gt 0 ]]; then
     mkdir -p "$FTYPE"/aux
     mv -f "$FTYPE"/*.NOTFOUND "$FTYPE"/aux/
diff --git a/scripts/preprocessing/prepro_move_preprocessed_files.sh b/scripts/preprocessing/prepro_move_preprocessed_files.sh
index 2429454..24614d0 100755
--- a/scripts/preprocessing/prepro_move_preprocessed_files.sh
+++ b/scripts/preprocessing/prepro_move_preprocessed_files.sh
@@ -11,7 +11,7 @@ fi
 FTYPE="$1"
 
 ANATYPE="${VERITAS_ANALYSIS_TYPE:0:2}"
-VERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFMINORVERSION)
+VERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFMINORVERSION)
 
 ODIR="$VERITAS_DATA_DIR/shared/processed_data_${VERSION}/${ANATYPE}/${FTYPE}"
 
@@ -23,9 +23,9 @@ for F in 11 10 9 8 7 6 5 4 3; do
     OFDIR="$ODIR/$F"
     echo "Syncing $OFDIR with ${FTYPE}"
     mkdir -p "$OFDIR"
-    NFIL=$(ls -1 ${FTYPE}/${F}*.root 2>/dev/null | wc -l)
+    NFIL=$(find "$FTYPE" -maxdepth 1 -name "${F}*.root" 2>/dev/null | wc -l)
     if [[ $NFIL -gt 0 ]]; then
-        rsync -av --remove-source-files ${FTYPE}/${F}*.root $OFDIR/
-        rsync -av --remove-source-files ${FTYPE}/${F}*.log $OFDIR/
+        rsync -av --remove-source-files "${FTYPE}"/${F}*.root "$OFDIR"/
+        rsync -av --remove-source-files "${FTYPE}"/${F}*.log "$OFDIR"/
     fi
 done
diff --git a/scripts/preprocessing/prepro_move_v2dl3_files.sh b/scripts/preprocessing/prepro_move_v2dl3_files.sh
index 3133978..0991859 100755
--- a/scripts/preprocessing/prepro_move_v2dl3_files.sh
+++ b/scripts/preprocessing/prepro_move_v2dl3_files.sh
@@ -14,17 +14,17 @@ DDIR="$2"
 
 ANATYPE="AP"
 ANATYPE="${VERITAS_ANALYSIS_TYPE:0:2}"
-VERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFMINORVERSION)
+VERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFMINORVERSION)
 
 ODIR="$VERITAS_DATA_DIR/shared/processed_data_${VERSION}/${ANATYPE}/"
 
 for F in 11 10 9 8 7 6 5 4 3; do
     OFDIR="$ODIR/$DDIR/$F"
     echo "Syncing $OFDIR with ${FTYPE}"
-    NFIL=$(ls -1 ${FTYPE}/${F}*.fits.gz 2>/dev/null | wc -l)
+    NFIL=$(find "$FTYPE" -maxdepth 1 -name "${F}*.fits.gz" 2>/dev/null | wc -l)
     if [[ $NFIL -gt 0 ]]; then
         mkdir -p "$OFDIR"
-        rsync -av --remove-source-files  ${FTYPE}/${F}*.fits.gz $ODIR/$DDIR/${F}/
-        rsync -av --remove-source-files  ${FTYPE}/${F}*.log $ODIR/$DDIR/${F}/
+        rsync -av --remove-source-files  "${FTYPE}"/${F}*.fits.gz "$ODIR"/"$DDIR"/${F}/
+        rsync -av --remove-source-files  "${FTYPE}"/${F}*.log "$ODIR"/"$DDIR"/${F}/
     fi
 done
diff --git a/scripts/preprocessing/prepro_pack_dl3_directories.sh b/scripts/preprocessing/prepro_pack_dl3_directories.sh
index 1851220..4f62315 100755
--- a/scripts/preprocessing/prepro_pack_dl3_directories.sh
+++ b/scripts/preprocessing/prepro_pack_dl3_directories.sh
@@ -10,5 +10,5 @@ echo "Pack DL3 for version $VERSION"
 for L in $LDIR
 do
     echo "Packing $L"
-    tar -czf ${L}-${VERSION}.tar.gz ${L} &
+    tar -czf "${L}"-${VERSION}.tar.gz "${L}" &
 done
diff --git a/scripts/preprocessing/prepro_rsync_data_ucla.sh b/scripts/preprocessing/prepro_rsync_data_ucla.sh
index d44c8ed..6083c36 100755
--- a/scripts/preprocessing/prepro_rsync_data_ucla.sh
+++ b/scripts/preprocessing/prepro_rsync_data_ucla.sh
@@ -18,7 +18,7 @@ if [[ ! -n "${VTS_UCLA_USER}" ]]; then
 fi
 
 USER="${VTS_UCLA_USER}"
-VERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFMINORVERSION)
+VERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFMINORVERSION)
 VERSION="v491.0"
 VERSION="v490.7"
 BACKUP="$1"
@@ -43,7 +43,7 @@ if [[ $SYNC_DL3TAR == "TRUE" ]]; then
     echo "Syncing DL3 tar ball"
     rsync -avz -e ssh \
          ./processed_data_${VERSION}/$ANATYPE/*.tar.gz \
-         ${USER}:/home/maierg/processed_Eventdisplay/${VERSION}/$ANATYPE/
+         "${USER}":/home/maierg/processed_Eventdisplay/${VERSION}/$ANATYPE/
 fi
 
 
@@ -51,14 +51,14 @@ if [[ $SYNC_DL3 == "TRUE" ]]; then
     echo "Syncing DL3 files"
     DLDIRS=$(find ./processed_data_${VERSION}/$ANATYPE/ -type d -name 'dl3_*')
     for DL in $DLDIRS; do
-         echo $DL
-         DL3=$(basename $DL)
+         echo "$DL"
+         DL3=$(basename "$DL")
          echo "SYNC with ${USER}:/home/maierg/processed_Eventdisplay/${VERSION}/$ANATYPE/$DL3/"
 
          rsync -avz -e ssh \
               --backup --suffix="$BACKUP" \
-              $DL/* \
-             ${USER}:/home/maierg/processed_Eventdisplay/${VERSION}/$ANATYPE/$DL3/
+              "$DL"/* \
+             "${USER}":/home/maierg/processed_Eventdisplay/${VERSION}/$ANATYPE/"$DL3"/
     done
 fi
 
@@ -67,7 +67,7 @@ if [[ $SYNC_MSCW == "TRUE" ]]; then
     rsync -avz -e ssh \
           --backup --suffix="$BACKUP" \
          ./processed_data_${VERSION}/$ANATYPE/mscw/* \
-         ${USER}:/home/maierg/processed_Eventdisplay/${VERSION}/$ANATYPE/mscw/
+         "${USER}":/home/maierg/processed_Eventdisplay/${VERSION}/$ANATYPE/mscw/
 fi
 
 
@@ -76,5 +76,5 @@ if [[ $SYNC_EVNDISP == "TRUE" ]]; then
     rsync -avz -e ssh \
          --backup --suffix="$BACKUP" \
         ./processed_data_${VERSION}/$ANATYPE/evndisp/* \
-        ${USER}:/home/maierg/processed_Eventdisplay/${VERSION}/$ANATYPE/evndisp/
+        "${USER}":/home/maierg/processed_Eventdisplay/${VERSION}/$ANATYPE/evndisp/
 fi
diff --git a/scripts/preprocessing/prepro_rsync_db_ucla.sh b/scripts/preprocessing/prepro_rsync_db_ucla.sh
index 6792420..8637a56 100755
--- a/scripts/preprocessing/prepro_rsync_db_ucla.sh
+++ b/scripts/preprocessing/prepro_rsync_db_ucla.sh
@@ -23,9 +23,9 @@ echo "USER: $USER BACKUP $BACKUP"
 rsync -avz -e ssh \
       --backup --suffix="$BACKUP" \
      ./DBFITS \
-     ${USER}:/home/maierg/processed_Eventdisplay/
+     "${USER}":/home/maierg/processed_Eventdisplay/
 
 rsync -avz -e ssh \
       --backup --suffix="$BACKUP" \
      ./DBTEXT \
-     ${USER}:/home/maierg/processed_Eventdisplay/
+     "${USER}":/home/maierg/processed_Eventdisplay/
diff --git a/scripts/preprocessing/print_dqm_string_from_runlist.sh b/scripts/preprocessing/print_dqm_string_from_runlist.sh
index a1eb43e..d1827b0 100755
--- a/scripts/preprocessing/print_dqm_string_from_runlist.sh
+++ b/scripts/preprocessing/print_dqm_string_from_runlist.sh
@@ -27,8 +27,8 @@ unpack_db_textdirectory()
     fi
     DBRUNFIL="${DBTEXTDIRECTORY}/${SRUN}/${RRUN}.tar.gz"
     if [[ -e ${DBRUNFIL} ]]; then
-        mkdir -p ${TMP_DBTEXTDIRECTORY}/
-        tar -xzf ${DBRUNFIL} -C ${TMP_DBTEXTDIRECTORY}/
+        mkdir -p "${TMP_DBTEXTDIRECTORY}"/
+        tar -xzf "${DBRUNFIL}" -C "${TMP_DBTEXTDIRECTORY}"/
     fi
     echo "${TMP_DBTEXTDIRECTORY}/${RRUN}/"
 }
@@ -57,9 +57,9 @@ do
         unpack_db_textdirectory "${R}" ./tmp_dbtext/ >/dev/null
         RDQM="./tmp_dbtext/${R}/${R}.rundqm"
         if [[ -e ${RDQM} ]]; then
-            RSTATUS=$(cut -d '|' -f 3 ${RDQM} | grep -v status)
-            RCUTMASK=$(cut -d '|' -f 7 ${RDQM} | grep -v status)
-            RCATEGORY=$(cut -d '|' -f 2 ${RDQM} | grep -v data_category)
+            RSTATUS=$(cut -d '|' -f 3 "${RDQM}" | grep -v status)
+            RCUTMASK=$(cut -d '|' -f 7 "${RDQM}" | grep -v status)
+            RCATEGORY=$(cut -d '|' -f 2 "${RDQM}" | grep -v data_category)
         else
             RSTATUS="NODQMFILE"
             RCUTMASK="NULL"
@@ -67,10 +67,10 @@ do
         fi
         RINF="./tmp_dbtext/${R}/${R}.runinfo"
         if [[ -e ${RINF} ]]; then
-            RLENGTH=$(cut -d '|' -f 9 ${RINF} | grep -v duration)
-            RWEATHER=$(cut -d '|' -f 10 ${RINF} | grep -v weather)
-            RTARGET=$(cut -d '|' -f 20 ${RINF} | grep -v source_id)
-            RTYPE=$(cut -d '|' -f 2 ${RINF} | grep -v run_type)
+            RLENGTH=$(cut -d '|' -f 9 "${RINF}" | grep -v duration)
+            RWEATHER=$(cut -d '|' -f 10 "${RINF}" | grep -v weather)
+            RTARGET=$(cut -d '|' -f 20 "${RINF}" | grep -v source_id)
+            RTYPE=$(cut -d '|' -f 2 "${RINF}" | grep -v run_type)
         else
             RLENGTH="NORUNINFOFILE"
             RWEATHER="NULL"
diff --git a/scripts/preprocessing/print_processed_runstatistics.sh b/scripts/preprocessing/print_processed_runstatistics.sh
index 254cddc..16da7a7 100755
--- a/scripts/preprocessing/print_processed_runstatistics.sh
+++ b/scripts/preprocessing/print_processed_runstatistics.sh
@@ -1,5 +1,4 @@
 #!/bin/bash
-# shellcheck disable=SC2034
 # Print processed run statistics for the different
 # stages of Eventdisplay
 
@@ -25,11 +24,11 @@ count_files()
     LL=0
 
     if [[ $1 == "V6" ]]; then
-        LL=$(find ${2} -name "*${3}" ! -name "*IPR.root" -exec basename {} "$3" \; | awk -F '-' '{if ($1 > 63372) print $0}' | wc -l)
+        LL=$(find "${2}" -name "*${3}" ! -name "*IPR.root" -exec basename {} "$3" \; | awk -F '-' '{if ($1 > 63372) print $0}' | wc -l)
     elif [[ $1 == "V4" ]]; then
-        LL=$(find ${2} -name "*${3}" ! -name "*IPR.root" -exec basename {} "$3" \; | awk -F '-' '{if ($1 > 1000 && $1 < 46642) print $1}' | wc -l)
+        LL=$(find "${2}" -name "*${3}" ! -name "*IPR.root" -exec basename {} "$3" \; | awk -F '-' '{if ($1 > 1000 && $1 < 46642) print $1}' | wc -l)
     elif [[ $1 == "V5" ]]; then
-        LL=$(find ${2} -name "*${3}" ! -name "*IPR.root" -exec basename {} "$3" \; | awk -F '-' '{if ($1 > 46641 && $1 < 63373) print $0}' | wc -l)
+        LL=$(find "${2}" -name "*${3}" ! -name "*IPR.root" -exec basename {} "$3" \; | awk -F '-' '{if ($1 > 46641 && $1 < 63373) print $0}' | wc -l)
     fi
     echo "$LL"
 }
@@ -37,15 +36,15 @@ count_files()
 for E in _V6 _V5 _V4
 do
     GLIST="$GOODFDIR/runlist${E}.dat"
-    GOODRUNS=$(cat ${GLIST} | wc -l)
+    GOODRUNS=$(cat "${GLIST}" | wc -l)
 
     for S in evndisp mscw
     do
         LL="0"
         if [[ $S == "evndisp" ]]; then
-            LL=$(count_files ${E:1} ${1}/${S}/ ".root")
+            LL=$(count_files ${E:1} "$FILEDIR"/${S}/ ".root")
         elif [[ $S == "mscw" ]]; then
-            LL=$(count_files ${E:1} ${1}/${S}/ ".mscw.root")
+            LL=$(count_files ${E:1} "$FILEDIR"/${S}/ ".mscw.root")
         fi
 
         echo "| ${E:1} | $S | ${GOODRUNS} | $LL |"
diff --git a/scripts/preprocessing/processing_dqm.sh b/scripts/preprocessing/processing_dqm.sh
index 57c7270..2825255 100755
--- a/scripts/preprocessing/processing_dqm.sh
+++ b/scripts/preprocessing/processing_dqm.sh
@@ -19,71 +19,71 @@ echo "Checking runs in ${1} for data type ${DTYPE}"
 check_evndisp_log_files()
 {
     # check number of log files of all stages
-    PNLOG=$(ls -1 ${1}/*.ped.log | wc -l)
-    TNLOG=$(ls -1 ${1}/*.tzero.log | wc -l)
-    ANLOG=$(ls -1 ${1}/*[0-9].log | wc -l)
+    PNLOG=$(find "$1" -maxdepth 1 -name "*.ped.log" | wc -l)
+    TNLOG=$(find "$1" -maxdepth 1 -name "*.tzero.log" | wc -l)
+    ANLOG=$(find "$1" -maxdepth 1 -name "*[0-9].log" | wc -l)
     echo "Number of log files: ped $PNLOG tzero $TNLOG evndisp $ANLOG"
     echo "Ped files: "
     echo "--------------------"
-    echo "   Container revisions: $(grep -h org.opencontainers.image.revision ${1}/*.ped.log | sort -u)"
-    echo "$(grep -i error ${1}/*.ped.log)"
+    echo "   Container revisions: $(grep -h org.opencontainers.image.revision "${1}"/*.ped.log | sort -u)"
+    echo "$(grep -i error "${1}"/*.ped.log)"
     echo "Tzero files: "
     echo "--------------------"
-    echo "   Container revisions: $(grep -h org.opencontainers.image.revision ${1}/*.tzero.log | sort -u)"
-    echo "$(grep -i error ${1}/*.tzero.log)"
+    echo "   Container revisions: $(grep -h org.opencontainers.image.revision "${1}"/*.tzero.log | sort -u)"
+    echo "$(grep -i error "${1}"/*.tzero.log)"
     echo "Evndisp files: "
     echo "--------------------"
-    echo "   Container revisions: $(grep -h org.opencontainers.image.revision ${1}/*[0-9].log | sort -u)"
-    echo "$(grep -i error ${1}/*[0-9].log)"
+    echo "   Container revisions: $(grep -h org.opencontainers.image.revision "${1}"/*[0-9].log | sort -u)"
+    echo "$(grep -i error "${1}"/*[0-9].log)"
     echo "Zero average pulse in evndisp files: "
     echo "--------------------"
-    echo "$(grep "average pulse timing for this telescope is 0" ${1}/*[0-9].log)"
+    echo "$(grep "average pulse timing for this telescope is 0" "${1}"/*[0-9].log)"
 #    echo "Warnings in evndisp files: "
 #    echo "--------------------"
 #    echo "$(grep -i warning ${1}/*[0-9].log | grep -v "WARNING: Skipping mount")"
-    grep -h -i EVNDISP.reconstruction.runparameter ${1}/*[0-9].log > $TMPLOG
+    grep -h -i EVNDISP.reconstruction.runparameter "${1}"/*[0-9].log > "$TMPLOG"
 }
 
 check_mscw_log_files()
 {
-    NFIL=$(ls -1 ${1}/*.mscw.root | wc -l)
+    NFIL=$(find "$1" -maxdepth 1 -name "*.mscw.root" | wc -l)
     echo "Number of mscw file: $NFIL"
-    echo "Container revisions: $(grep -h org.opencontainers.image.revision ${1}/*.mscw.log | sort -u)"
+    echo "Container revisions: $(grep -h org.opencontainers.image.revision "${1}"/*.mscw.log | sort -u)"
     echo "Errors in mscw log files:"
-    echo "$(grep -i error ${1}/*.mscw.log |  grep -v "error weighting parameter" | grep -v BDTDispError | grep -v "disp error")"
-    grep -h -i "lookuptable:" ${1}/*[0-9].mscw.log > $TMPLOG
+    echo "$(grep -i error "${1}"/*.mscw.log |  grep -v "error weighting parameter" | grep -v BDTDispError | grep -v "disp error")"
+    grep -h -i "lookuptable:" "${1}"/*[0-9].mscw.log > "$TMPLOG"
 }
 
 check_anasum_log_files()
 {
-    NFIL=$(find ${1} -name "*.anasum.root" | wc -l)
+    NFIL=$(find "${1}" -name "*.anasum.root" | wc -l)
     echo "Number of anasum file: $NFIL"
-    echo "Container revisions: $(find ${1} -name "*.anasum.log" -exec grep -h org.opencontainers.image.revision {} \; | sort -u)"
+    echo "Container revisions: $(find "${1}" -name "*.anasum.log" -exec grep -h org.opencontainers.image.revision {} \; | sort -u)"
     echo "Errors in anasumlog files:"
-    echo "$(find ${1} -name "*.anasum.log" -exec grep -H -i error {} \;)"
-    find ${1} -name "*.anasum.log" -exec grep -h -i "reading effective areas from" {} \;> $TMPLOG
+    echo "$(find "${1}" -name "*.anasum.log" -exec grep -H -i error {} \;)"
+    find "${1}" -name "*.anasum.log" -exec grep -h -i "reading effective areas from" {} \;> "$TMPLOG"
 }
 
 check_v2dl3_log_files()
 {
-    NFIL=$(find ${1}/point-like -name "*.fits.gz" | wc -l)
+    NFIL=$(find "${1}"/point-like -name "*.fits.gz" | wc -l)
     echo "Number of v2dl3 file: $NFIL"
     echo "Errors in v2dl3 files:"
-    echo "$(find ${1} -name "*.log" -exec grep -H -i error {} \; | grep -v "several offsets" | grep -v "Coordinate zenith tolerance is")"
+    echo "$(find "${1}" -name "*.log" -exec grep -H -i error {} \; | grep -v "several offsets" | grep -v "Coordinate zenith tolerance is")"
 }
 
 TMPLOG="$(pwd)/DQM.${DTYPE}.$(uuid).tmp.txt"
-rm -f $TMPLOG
+rm -f "$TMPLOG"
 if [[ $DTYPE == "evndisp" ]]; then
-    check_evndisp_log_files $FDIR
-    cat $TMPLOG | sort -u
+    check_evndisp_log_files "$FDIR"
+    cat "$TMPLOG" | sort -u
 elif [[ $DTYPE == "mscw" ]]; then
-    check_mscw_log_files $FDIR
-    cat $TMPLOG | sort -u
+    check_mscw_log_files "$FDIR"
+    cat "$TMPLOG" | sort -u
 elif [[ $DTYPE == "anasum" ]]; then
-    check_anasum_log_files $FDIR
-    cat $TMPLOG | sort -u
+    check_anasum_log_files "$FDIR"
+    cat "$TMPLOG" | sort -u
 elif [[ $DTYPE == "v2dl3" ]]; then
-    check_v2dl3_log_files $FDIR
+    check_v2dl3_log_files "$FDIR"
 fi
-rm -f $TMPLOG
+rm -f "$TMPLOG"
diff --git a/scripts/set_environment.sh b/scripts/set_environment.sh
index a5fe6ec..6672bca 100755
--- a/scripts/set_environment.sh
+++ b/scripts/set_environment.sh
@@ -68,16 +68,18 @@ if [[ $PROCESS == "apptainer"* ]]; then
     # Alma Linux 9 (al9) processing
 elif [[ $PROCESS == "al9" ]]; then
     unset EVNDISP_APPTAINER
-    TDIR=`pwd`
+    TDIR=$(pwd)
     export ROOTSYS=/afs/ifh.de/group/cta/cta/software/root/root_v6.30.02.Linux-almalinux9.3-x86_64-gcc11.4/
     export VBFSYS=/afs/ifh.de/group/cta/VERITAS/software/VBF-0.3.4-c17/
     export EVNDISPSYS=${USERAFSDIR}/EVNDISP/EVNDISP-400/GITHUB_Eventdisplay/EventDisplay_${EVNDISPVERSION:0:4}-${PROCESS}
     cd "$ROOTSYS" || return
+# shellcheck source=/dev/null
     source ./bin/thisroot.sh
     export PATH=$PATH:${VBFSYS}/bin/
     export LD_LIBRARY_PATH="$VBFSYS/lib:$LD_LIBRARY_PATH"
     export SOFASYS=${EVNDISPSYS}/sofa
     cd "${EVNDISPSYS}" || return
+# shellcheck source=/dev/null
     source ./setObservatory.sh VTS
     cd "${TDIR}" || return
 fi