fastp/workflow.wdl

import "./tasks/fastp.wdl" as fastp
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: 
		sample_id=quartet[2],
		read1=quartet[0], 
		read2=quartet[1],
		docker = fastp_docker,
		cluster = fastp_cluster
		}
	}
}