......

tasks/fastp.wdl

@@ -29,7 +29,8 @@ task fastp {
 	mv ${read2} {sample_id}_R2.fastq.tmp1.gz
         else
 	fastp --thread 4 --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i ${read1} -I ${read2} -o ${sample_id}_R1.fastq.tmp1.gz -O ${sample_id}_R2.fastq.tmp1.gz -j ${sample_id}.json -h ${sample_id}.html
-
+        fi
+        
 	##2.UMI
 	if [ ${UMI} -gt 0 ]
         then
@@ -37,11 +38,20 @@ task fastp {
 	mv ${sample_id}_R2.fastq.tmp1.gz ${sample_id}_R2.fastq.tmp2.gz
         else
 	fastp --thread 4 -U --umi_loc=${umi_loc} --umi_len=${umi_len} --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i ${sample_id}_R1.fastq.tmp1.gz -I ${sample_id}_R2.fastq.tmp1.gz -o ${sample_id}_R1.fastq.tmp2.gz -O ${sample_id}_R2.fastq.tmp2.gz -j ${sample_id}.json -h ${sample_id}.html
-	
+	fi
+
 	##3.Trim
         if [ ${disable_adapter_trimming} -gt 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} --detect_adapter_for_pe --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i ${sample_id}_R1.fastq.tmp2.gz -I ${sample_id}_R2.fastq.tmp2.gz -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.fastq.gz -j ${sample_id}.json -h ${sample_id}.html
+	fastp --thread 4 -l ${length_required} -q ${qualified_quality_phred} -u ${length_required1}  /
+        --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} /
+        --detect_adapter_for_pe /
+        --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1}  /
+        --max_len1 ${max_len1} --trim_front2 ${trim_front2}  /
+        --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} /
+         -i ${sample_id}_R1.fastq.tmp2.gz -I ${sample_id}_R2.fastq.tmp2.gz /
+          -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.fastq.gz / 
+          -j ${sample_id}.json -h ${sample_id}.html
         else
 	mv ${sample_id}_R1.fastq.tmp2.gz ${sample_id}_R1.fastq.gz
 	mv ${sample_id}_R2.fastq.tmp2.gz ${sample_id}_R2.fastq.gz