first commit

defaults

@@ -28,6 +28,7 @@
     "max_intronlen":"500000",
     "maxins":"500",
     "minins":"0",
+    "length_limit":"30",
     "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
     "samtools_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
     "insert_size":"8000",

tasks/fastp.wdl

@@ -16,6 +16,7 @@ task fastp {
     Int qualified_quality_phred
     Int length_required1
     Int disable_quality_filtering
+    Int length_limit
    
 	command <<<
         mkdir -p /cromwell_root/tmp/fastp/
@@ -38,7 +39,7 @@ 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} --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} --length_limit ${length_limit} --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

workflow.wdl

@@ -66,6 +66,7 @@ workflow {{ project_name }} {
 	String disk_size
 	String count_docker
 	String count_cluster
+	Int length_limit
 
 	call fastp.fastp as fastp {
 		input: