import "./tasks/fastp.wdl" as fastp
import "./tasks/hisat2.wdl" as hisat2
import "./tasks/samtools.wdl" as samtools
import "./tasks/stringtie.wdl" as stringtie
import "./tasks/fastqc.wdl" as fastqc
import "./tasks/fastqscreen.wdl" as fastqscreen
import "./tasks/qualimapBAMqc.wdl" as qualimapBAMqc
import "./tasks/qualimapRNAseq.wdl" as qualimapRNAseq
import "./tasks/multiqc.wdl" as multiqc

workflow {{ project_name }} {
	
	
	String stringtie_docker
	String stringtie_cluster
	String multiqc_cluster_config
	String multiqc_docker
	Int multiqc_disk_size
	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
	
}