RNA_Datapotal/workflow.wdl

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
	Int qualified_quality_phred
	Int length_required1
	Int disable_quality_filtering
	Int pen_cansplice
	Int pen_noncansplice
	Int min_intronlen
	Int max_intronlen
	Int maxins
	Int minins
	Int fastqc_disk_size
	Int fastqscreen_disk_size
	Int qualimapBAMqc_disk_size
	Int qualimapRNAseq_disk_size
	Int insert_size
	Int minimum_length_allowed_for_the_predicted_transcripts
    	Int Junctions_no_spliced_reads
   	Float minimum_isoform_abundance
    	Float maximum_fraction_of_muliplelocationmapped_reads
}