FastQC/workflow.wdl

import "./tasks/fastp.wdl" as fastp
import "./tasks/fastqscreen.wdl" as fastqscreen

workflow {{ project_name }} {
    File in1
    File in2
    String sample_id
    File screen_ref_dir
    File fastq_screen_conf
    String docker_fastp
    String docker_fastqscreen
    String cluster_config
    String disk_size


	call fastp.fastp as fastp{
		input:
			in1=in1,
			in2=in2,
			sample_id=sample_id,
			docker=docker_fastp,
			cluster_config=cluster_config,
			disk_size=disk_size
			
	
	}

    call fastqscreen.fastq_screen as fastq_screen{
		input:
			read1=in1,
			read2=in2,
			sample=sample_id,
			docker=docker_fastqscreen,
			cluster_config=cluster_config,
			screen_ref_dir = screen_ref_dir,
            fastq_screen_conf = fastq_screen_conf,
			disk_size=disk_size
			
	
	}

	

}