......

defaults

@@ -42,5 +42,5 @@
     "umi_len": "0", 
     "umi_loc": "umi_loc", 
     "qualified_quality_phred": "20", 
-    "disable_quality_filtering": "0"
+    "disable_quality_filtering": "1"
 }

tasks/fastp.wdl

@@ -22,22 +22,23 @@ task fastp {
     Int disable_quality_filtering
    
 	command <<<
+        mkdir -p /cromwell_root/tmp/fastp/
 	##1.Disable_quality_filtering
 	if [ ${disable_quality_filtering} -gt 0 ]
         then
-	mv ${read1} {sample_id}_R1.fastq.tmp1.gz
-	mv ${read2} {sample_id}_R2.fastq.tmp1.gz
+	cp ${read1} /cromwell_root/tmp/fastp/{sample_id}_R1.fastq.tmp1.gz
+	cp ${read2} /cromwell_root/tmp/fastp/{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
+	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 ${read2} -o /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp1.gz -O /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp1.gz -j ${sample_id}.json -h ${sample_id}.html
         fi
-        
+
 	##2.UMI
 	if [ ${UMI} -gt 0 ]
         then
-	mv ${sample_id}_R1.fastq.tmp1.gz ${sample_id}_R1.fastq.tmp2.gz
-	mv ${sample_id}_R2.fastq.tmp1.gz ${sample_id}_R2.fastq.tmp2.gz
+	cp /cromwell_root/tmp/fastp/${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/${sample_id}_R2.fastq.tmp2.gz
         else
-	fastp --thread 4 -U --umi_loc=${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 ${sample_id}.html
+	fastp --thread 4 -U --umi_loc=${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 ${max_len2} -i /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp1.gz -I /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp1.gz -o /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz -O /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp2.gz -j ${sample_id}.json -h ${sample_id}.html
 	fi
 
 	##3.Trim
@@ -49,12 +50,12 @@ task fastp {
         --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 ${sample_id}.html
+        -i /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz -I /cromwell_root/tmp/fastp/${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 ${sample_id}_R2.fastq.gz
+	cp /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz ${sample_id}_R1.fastq.gz
+	cp /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp2.gz ${sample_id}_R2.fastq.gz
         fi
    >>>