......

tasks/fastp.wdl

@@ -49,8 +49,8 @@ task fastp {
    >>>
    
    runtime { 
-		docker: fastp_docker
-		cluster: fastp_cluster
+		docker: docker
+		cluster: cluster
 		systemDisk: "cloud_ssd 40"
 		dataDisk: "cloud_ssd 200 /cromwell_root/"
    }

workflow.wdl

@@ -3,7 +3,24 @@ workflow {{ project_name }} {
 	File inputSamplesFile
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
 	String fastp_docker
+	String adapter_sequence
+	String adapter_sequence_r2
 	String fastp_cluster
+	String umi_loc	
+	Int trim_front1 
+	Int trim_tail1 
+	Int max_len1 
+	Int trim_front2 
+	Int trim_tail2  
+	Int max_len2 
+	Int disable_adapter_trimming
+	Int length_required
+	Int umi_len
+	Int UMI
+	Int qualified_quality_phred
+	Int length_required1
+	Int disable_quality_filtering
+
 	scatter (quartet in inputSamples){
 		call fastp.fastp as fastp {
 		input: