first commit

defaults

@@ -9,7 +9,7 @@
     "max_len2": "0",
     "adapter_sequence": "TGGAATTCTCGGGTGCCAAGG",
     "disable_adapter_trimming": "0",
-    "length_required": "50",
+    "length_required": "15",
     "length_required1": "20",
     "UMI": "0",
     "umi_len": "0",

tasks/fastp.wdl

@@ -38,7 +38,7 @@ task fastp {
 	##3.Trim
         if [ "${disable_adapter_trimming}" == 0 ]
         then
-	fastp --thread 4 -l ${length_required} -q ${qualified_quality_phred} -u ${length_required1} --adapter_sequence ${adapter_sequence} --detect_adapter_for_pe --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} -i /cromwell_root/tmp/fastp/${sample_id}.fastq.tmp2.gz -o ${sample_id}.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 --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} -i /cromwell_root/tmp/fastp/${sample_id}.fastq.tmp2.gz -o ${sample_id}.fastq.gz -j ${sample_id}.json -h ${sample_id}.html
         else
 	cp /cromwell_root/tmp/fastp/${sample_id}.fastq.tmp2.gz ${sample_id}.fastq.gz
         fi