Merge pull request #272 from RoanKanninga/master

put quotes around variable in a comparison

compute5/NGS_DNA-3.0.2/protocols/BwaAlign.sh

@@ -28,7 +28,7 @@ ${checkStage}
 READGROUPLINE="@RG\tID:${lane}\tPL:illumina\tLB:${filePrefix}\tSM:${externalSampleID}"
 
 #If paired-end use two fq files as input, else only one
-if [ ${seqType} == "PE" ]
+if [ "${seqType}" == "PE" ]
 then
     #Run BWA for paired-end
     bwa mem \

compute5/NGS_DNA-3.0.2/protocols/CheckIlluminaEncoding.sh

@@ -33,7 +33,7 @@ do
             	count=$(( count++ ))
         	fi
 
-        	if ! [ ${encoding} == ${lastEncoding} ]
+        	if ! [ "${encoding}" == "${lastEncoding}" ]
         	then
 	            	echo "error, encoding not possible"
 			echo "${encoding} is not matching last encoding (${lastEncoding}"
@@ -51,28 +51,28 @@ do
         		lastEncoding=${encoding}
 	        	count=$(( count++ ))
         	fi
-        	if ! [ ${encoding} == ${lastEncoding} ]
+        	if ! [ "${encoding}" == "${lastEncoding}" ]
         	then
                 	echo "error, encoding not possible"
 			echo "${encoding} is not matching last encoding (${lastEncoding}"
 			echo "LINE: " $line
 	                exit 1
                 fi
-              	lastEncoding=${encoding}
+              	lastEncoding="${encoding}"
 	elif [[ "$line" =~ @ ]] || [[ "$line" =~ [A-J] ]]
         	then
                 nodecision=$(( nodecision++ ))
 	else
 		echo "The encoding is not matching to anything, check FastQ documentation (count=$count)"
 	fi
 done
-if [ $nodecision == $numberoflines ]
+if [ "${nodecision}" == "${numberoflines}" ]
 then
 	echo "Within all the lines, no decision was made about the encoding, all the encoding is between A and J. This is then probably an 1.9 encoding sample, so 1.9 is set as encoding"
 	encoding="1.9"
 fi
 
-if [ ${encoding} == "1.9"  ]
+if [ "${encoding}" == "1.9"  ]
 then
 	echo "encoding is Illumina 1.8 - Sanger / Illumina 1.9"
 else
@@ -92,11 +92,11 @@ fi
 #check illumina encoding using function checkIlluminaEncoding()
 
 #If paired-end do fastqc for both ends, else only for one
-if [ ${seqType} == "SR" ]
+if [ "${seqType}" == "SR" ]
 then
         checkIlluminaEncoding ${srBarcodeFqGz}
 
-elif [ $seqType == "PE" ]
+elif [ "${seqType}" == "PE" ]
 then
         checkIlluminaEncoding ${peEnd1BarcodeFqGz}
         checkIlluminaEncoding ${peEnd2BarcodeFqGz}

compute5/NGS_DNA-3.0.2/protocols/CollectBamMetrics.sh

@@ -56,7 +56,7 @@ TMP_DIR=${tempDir}
     mv ${tmpCollectBamMetricsPrefix}.quality_by_cycle.pdf ${inputCollectBamMetricsBam}.quality_by_cycle.pdf
 
     #If paired-end data *.insert_size_metrics files also need to be moved
-    if [ ${seqType} == "PE" ]
+    if [ "${seqType}" == "PE" ]
 	then
 	echo -e "\nDetected paired-end data, moving all files.\n\n"
     mv ${tmpCollectBamMetricsPrefix}.insert_size_metrics ${inputCollectBamMetricsBam}.insert_size_metrics
@@ -82,7 +82,7 @@ TMP_DIR=${tempDir}
 
 ######IS THIS STILL NEEDED, IMPROVEMENTS/UPDATES TO BE DONE?#####
 #Create nicer insertsize plots if seqType is PE
-#if [ ${seqType} == "PE" ]
+#if [ "${seqType}" == "PE" ]
 #then
 	# Overwrite the PDFs that were just created by nicer onces:
 	${recreateInsertSizePdfR} \
@@ -99,7 +99,7 @@ TMP_DIR=${tempDir}
 #####THIS "FAKE" FILE SHOULDN'T BE NEEDED, PLEASE FIX IN NEXT PIPELINE VERSION#####
 
 #Run Picard HsMetrics if capturingKit was used
-if [ ${capturingKit} != "None" ]
+if [ "${capturingKit}" != "None" ]
 then
 	java -jar -Xmx4g ${EBROOTPICARD}/${picardJar} ${hsMetricsJar} \
 	INPUT=${inputCollectBamMetricsBam} \

compute5/NGS_DNA-3.0.2/protocols/CountAllFinishedFiles.sh

@@ -12,7 +12,7 @@ countShScripts=$(($countShScripts-3))
 
 rm -f ${projectJobsDir}/${taskId}_INCORRECT
 
-if (( $countShScripts == $countFinishedFiles ))
+if [ "${countShScripts}" == "$countFinishedFiles" ]
 then	
 	echo "all files are finished" > ${projectJobsDir}/${taskId}_CORRECT
 else

compute5/NGS_DNA-3.0.2/protocols/CoveragePerBase.sh

@@ -15,7 +15,7 @@
 sleep 5
 module load ${gatkVersion}
 
-if [ $GCC_Analysis == "diagnostiek" ] || [ $GCC_Analysis == "diagnostics" ]
+if [ "${GCC_Analysis}" == "diagnostiek" ] || [ "${GCC_Analysis}" == "diagnostics" ]
 then
 	if [ -f ${capturedIntervalsPerBase} ]
 	then

compute5/NGS_DNA-3.0.2/protocols/FastQC.sh

@@ -21,7 +21,7 @@ makeTmpDir ${intermediateDir}
 tmpIntermediateDir=${MC_tmpFile}
 
 #If paired-end do fastqc for both ends, else only for one
-if [ ${seqType} == "PE" ]
+if [ "${seqType}" == "PE" ]
 then
 	fastqc ${peEnd1BarcodeFqGz} \
 	${peEnd2BarcodeFqGz} \

compute5/NGS_DNA-3.0.2/protocols/IndelFiltration.sh

@@ -21,7 +21,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${array[@]}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/MergeBam.sh

@@ -22,7 +22,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/MergeBatches.sh

@@ -36,7 +36,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/MergeIndelsAndSnps.sh

@@ -15,7 +15,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/Pindel.sh

@@ -35,7 +35,7 @@ configFile=${intermediateDir}/${externalSampleID}.pindel.config.txt
 
 
 echo "${bamFilePindel} ${targetedInsertSize} ${externalSampleID}" > ${configFile}
-if [ ${seqType} == "PE" ]
+if [ "${seqType}" == "PE" ]
 then
 	pindel \
 	-f ${indexFile} \
@@ -71,7 +71,7 @@ then
 perl /gcc/tools/scripts/filterPindelVcf.pl ${pindelOutputVcf}.tmp ${pindelOutputVcf}
 
 
-elif [ ${seqType} == "SR" ] 
+elif [ "${seqType}" == "SR" ] 
 then
 	echo "Pindel step is skipped because it is not Paired End but the seqType="${seqType}
 fi

compute5/NGS_DNA-3.0.2/protocols/QCReport.sh

@@ -56,7 +56,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/SequenomConcordanceCheck.sh

@@ -106,7 +106,7 @@ else
 	sed -e 's/chr//' ${sample}.genotypeArray.vcf | awk '{OFS="\t"; if (!/^#/){print $1,$2-1,$2}}' \
 	> ${sample}.genotypeArray.bed
 
-if [ $build == "build37" ]
+if [ "${build}" == "build37" ]
 then
 		###################################
 	#Sequonomfile is on build 37
@@ -193,11 +193,11 @@ then
 		--comp comp_immuno \
 		--header >> ${sampleConcordanceFile}		
 	fi
-	if [ $build == "N/A" ]
+	if [ "${build}" == "N/A" ]
 	then
  		echo "ERROR: unsure which build was used. None of the probes we checked was found in the array file."
  	fi
- 	if [ $build == "ERROR" ]
+ 	if [ "${build}" == "ERROR" ]
  	then
  		echo "ERROR: one of the probe in the array file has an unexpected position. Therefore, we are not able to tell which build was used." 
 	fi

compute5/NGS_DNA-3.0.2/protocols/SnpEff.sh

@@ -31,7 +31,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/SnpFiltration.sh

@@ -21,7 +21,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${array[@]}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/SnpVQSRFiltration.sh

@@ -21,7 +21,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${array[@]}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/SpikePhiX.sh

@@ -20,11 +20,11 @@ then
 	echo "Skip this step! PhiX was already spiked in!"
 	exit 0
 else
-	if [ ${seqType} == "SR" ]
+	if [ "${seqType}" == "SR" ]
 	then
 		echo "Spike phiX not implemented yet for Single Read"
 		exit 1
-	elif [ $seqType == "PE" ]
+	elif [ "${seqType}" == "PE" ]
 	then
 		echo "Append phiX reads"
 		cat ${peEnd1BarcodeFqGz} ${phiXEnd1Gz} > ${peEnd1BarcodeFqGz}.tmp

compute5/NGS_DNA-3.0.2/protocols/SplitIndelsAndSNPs.sh

@@ -24,7 +24,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/VariantAnnotator.sh

@@ -44,7 +44,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/VariantGVCFCalling.sh

@@ -30,7 +30,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi
@@ -75,14 +75,14 @@ baitBatchLength=`cat ${capturedBatchBed} | wc -l`
 bams=($(printf '%s\n' "${realignedBam[@]}" | sort -u ))
 inputs=$(printf ' -I %s ' $(printf '%s\n' ${bams[@]}))
 
-if [ ${baitBatchLength} == 0 ]
+if [ ${baitBatchLength} -eq 0 ]
 then
 	echo "skipped ${capturedBatchBed}, because the batch is empty"  
 else
 	if [[ ${capturedBatchBed} == *batch-[0-9]*X.bed ]]
 	then
 
-		if [ ${sex} == "Male" ]
+		if [ "${sex}" == "Male" ]
 		then
 			echo "X (male): NON AUTOSOMAL REGION"
 			java -Xmx12g -XX:ParallelGCThreads=2 -Djava.io.tmpdir=${tempDir} -jar \
@@ -98,7 +98,7 @@ else
 			-L ${capturedBatchBed} \
 			--emitRefConfidence GVCF \
 			-ploidy 1
-		elif [ ${sex} == "Female" ]
+		elif [ "${sex}" == "Female" ]
 		then
 			echo "X (female)"
 			#Run GATK HaplotypeCaller in DISCOVERY mode to call SNPs and indels
@@ -116,13 +116,13 @@ else
         		--emitRefConfidence GVCF \
 			-ploidy 2 
 		fi
-	elif [[ $capturedBatchBed == *batch-[0-9]*Y.bed ]]
+	elif [[ "${capturedBatchBed}" == *batch-[0-9]*Y.bed ]]
 	then
 		echo "Y"
-		if [ ${sex} == "Female" ]
+		if [ "${sex}" == "Female" ]
         	then
         	        echo "This sample is not a male, chromosome Y skipped!"
-        	elif [ ${sex} == "Male" ]
+        	elif [ "${sex}" == "Male" ]
 		then
 			java -Xmx12g -XX:ParallelGCThreads=2 -Djava.io.tmpdir=${tempDir} -jar \
                         ${EBROOTGATK}/${gatkJar} \
@@ -155,9 +155,9 @@ else
                 -ploidy 2
 	fi
 
-	if [[ $capturedBatchBed == *batch-[0-9]*X.bed ]]
+	if [[ "${capturedBatchBed}" == *batch-[0-9]*X.bed ]]
 	then
-		if [ -f ${tmpSampleBatchVariantCallsMaleNONPAR} ] && [ -f  ${tmpSampleBatchVariantCallsFemale} ]
+		if [ -f "${tmpSampleBatchVariantCallsMaleNONPAR}" ] && [ -f  "${tmpSampleBatchVariantCallsFemale}" ]
 		then
 			echo "combine male and female chrX"
 			java -Xmx2g -jar ${EBROOTGATK}/${gatkJar} \
@@ -168,12 +168,12 @@ else
    			--variant ${tmpSampleBatchVariantCallsFemale} \
 			-o ${tmpSampleBatchVariantCalls}
 
-		elif [ ! -f ${tmpSampleBatchVariantCallsMaleNONPAR} ]  
+		elif [ ! -f "${tmpSampleBatchVariantCallsMaleNONPAR}" ]  
 		then
 			echo "There are no males"
 			tmpSampleBatchVariantCalls=${tmpSampleBatchVariantCallsFemale}
 			tmpSampleBatchVariantCallsIdx=${tmpSampleBatchVariantCallsFemaleIdx}
-		elif [ ! -f ${tmpSampleBatchVariantCallsFemale} ]
+		elif [ ! -f "${tmpSampleBatchVariantCallsFemale}" ]
         	then
 			echo "There are no females!"
                 	tmpSampleBatchVariantCalls=${tmpSampleBatchVariantCallsMaleNONPAR}
@@ -184,7 +184,7 @@ else
 	fi
 
 	echo -e "\nVariantCalling finished succesfull. Moving temp files to final.\n\n"
-	if [ -f ${tmpSampleBatchVariantCalls} ]
+	if [ -f "${tmpSampleBatchVariantCalls}" ]
 	then
         	mv ${tmpSampleBatchVariantCalls} ${sampleBatchVariantCalls}
         	mv ${tmpSampleBatchVariantCallsIdx} ${sampleBatchVariantCallsIdx}

compute5/NGS_DNA-3.0.2/protocols/VariantGVCFCombine.sh

@@ -22,7 +22,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/VariantGVCFGenotyping.sh

@@ -24,7 +24,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/VcfToTable.sh

@@ -19,7 +19,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi

compute5/NGS_DNA-3.0.2/protocols/dbNSFPAnnotation.sh

@@ -66,7 +66,7 @@ array_contains () {
     local seeking=$2
     local in=1
     for element in "${!array-}"; do
-        if [[ $element == $seeking ]]; then
+        if [[ "$element" == "$seeking" ]]; then
             in=0
             break
         fi
@@ -94,7 +94,7 @@ ${variantAnnotatorSampleOutputSnpsFilteredVcf} > ${tmpDbNSFPSampleVcf}
 
 FIRSTLINE=`head -1 ${tmpDbNSFPSampleVcf}`
 
-if [[ $FIRSTLINE == *"hg38"* ]]
+if [[ "$FIRSTLINE" == *"hg38"* ]]
 then
 	sed '1d' ${tmpDbNSFPSampleVcf} > ${dbNSFPSampleVcf}
 	echo "removed first line of ${tmpDbNSFPSampleVcf} and moved file to ${dbNSFPSampleVcf}"