......

tasks/fastp.wdl

@@ -24,7 +24,7 @@ task fastp {
 	command <<<
         mkdir -p /cromwell_root/tmp/fastp/
 	##1.Disable_quality_filtering
-	if [ ${disable_quality_filtering} -gt 0 ]
+	if [ "${disable_quality_filtering}" == 0 ]
         then
 	cp ${read1} /cromwell_root/tmp/fastp/{sample_id}_R1.fastq.tmp1.gz
 	cp ${read2} /cromwell_root/tmp/fastp/{sample_id}_R2.fastq.tmp1.gz
@@ -33,7 +33,7 @@ task fastp {
         fi
 
 	##2.UMI
-	if [ ${UMI} -gt 0 ]
+	if [ "${UMI}" == 0 ]
         then
 	cp /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp1.gz /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz
 	cp /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp1.gz /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp2.gz
@@ -42,7 +42,7 @@ task fastp {
 	fi
 
 	##3.Trim
-        if [ ${disable_adapter_trimming} -gt 0 ]
+        if [ "${disable_adapter_trimming}" == 0 ]
         then
 	fastp --thread 4 -l ${length_required} -q ${qualified_quality_phred} -u ${length_required1}  /
         --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} /