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/multiqc.wdl" as multiqc

workflow {{ project_name }} {
	
	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	
	String fasta
	String idx_prefix
	File screen_ref_dir
	File fastq_screen_conf
    	File idx
	File gtf
	File ref_dir


	scatter (quartet in inputSamples){

		call fastp.fastp as fastp {
		input: 
		sample_id=quartet[2],
		read1=quartet[0], 
		read2=quartet[1], 
		adapter_sequence=quartet[3], 
		adapter_sequence_r2=quartet[4]
		}

		call fastqc.fastqc as fastqc {
		input:
		read1=fastp.Trim_R1, 
		read2=fastp.Trim_R2
		}

		call fastqscreen.fastq_screen as fastqscreen {
		input:
		read1=fastp.Trim_R1, 
		read2=fastp.Trim_R2,
		screen_ref_dir=screen_ref_dir,
		fastq_screen_conf=fastq_screen_conf
		}

		call hisat2.hisat2 as hisat2 {
		input: 
		sample_id=quartet[2],
		idx=idx, 
		idx_prefix=idx_prefix, 
		Trim_R1=fastp.Trim_R1, 
		Trim_R2=fastp.Trim_R2
		}

		call samtools.samtools as samtools {
		input: 
		sample_id=quartet[2],
		sam = hisat2.sam 
            	}
        
        	call qualimapBAMqc.qualimapBAMqc as qualimapBAMqc {
		input:
		bam= samtools.out_bam
		}


		call stringtie.stringtie as stringtie {
		input: 
		sample_id = quartet[2],
		gtf = gtf, 
		bam = samtools.out_bam
		}
	}


	call multiqc.multiqc as multiqc {
	input:
	read1_zip = fastqc.read1_zip,
	read2_zip = fastqc.read2_zip,
	txt1 = fastqscreen.txt1,
	txt2 = fastqscreen.txt2,
	bamqc_zip = qualimapBAMqc.bamqc_zip
	}
}