......

inputs

@@ -11,7 +11,7 @@
 	"{{ project_name }}.adapter_sequence": "{{ adapter_sequence }}",
 	"{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}",
 	"{{ project_name }}.disable_adapter_trimming": "{{ disable_adapter_trimming }}",
-	"{{ project_name }}.length_required": "{{ length_required }}",
+	"{{ project_name }}.length_required1": "{{ length_required1 }}",
 	"{{ project_name }}.UMI": "{{ UMI }}",
 	"{{ project_name }}.umi_loc": "{{ umi_loc }}",
 	"{{ project_name }}.umi_len": "{{ umi_len }}",

workflow.wdl

@@ -96,7 +96,10 @@ workflow {{ project_name }} {
 		call fastqc.fastqc as fastqc {
 		input:
 		read1=fastp.Trim_R1, 
-		read2=fastp.Trim_R2
+		read2=fastp.Trim_R2,
+		docker=fastqc_docker,
+		cluster_config=fastqc_cluster_config,
+		disk_size=fastqc_cluster_config
 		}
 
 		call fastqscreen.fastq_screen as fastqscreen {
@@ -104,7 +107,10 @@ workflow {{ project_name }} {
 		read1=fastp.Trim_R1, 
 		read2=fastp.Trim_R2,
 		screen_ref_dir=screen_ref_dir,
-		fastq_screen_conf=fastq_screen_conf
+		fastq_screen_conf=fastq_screen_conf,
+		docker = fastqscreen_docker,
+		cluster_config = fastqscreen_cluster_config,
+		disk_size= fastqscreen_disk_size
 		}
 
 		call hisat2.hisat2 as hisat2 {
@@ -168,6 +174,9 @@ workflow {{ project_name }} {
 
 	call multiqc.multiqc as multiqc {
 	input:
+	docker = multiqc_docker,
+	cluster_config = multiqc_cluster_config,
+	disk_size = multiqc_disk_size,
 	read1_zip = fastqc.read1_zip,
 	read2_zip = fastqc.read2_zip,
 	txt1 = fastqscreen.txt1,