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 }} {

	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	File screen_ref_dir
	File fastq_screen_conf
	File ref_dir
	File gtf
	String fasta

	scatter (sample in inputSamples) {
		call fastqc.fastqc as fastqc {
			input:
			read1=sample[0],
			read2=sample[1]
		}

		call fastqscreen.fastq_screen as fastqscreen {
			input:
			read1=sample[0],
			read2=sample[1],
			screen_ref_dir=screen_ref_dir,
			fastq_screen_conf=fastq_screen_conf
		}

		call qualimapBAMqc.qualimapBAMqc as qualimapBAMqc {
			input:
			bam=sample[2],
			bai=sample[3]
		}

		call qualimapRNAseq.qualimapRNAseq as qualimapRNAseq {
			input:
			bam=sample[2],
			bai=sample[3],
			gtf=gtf		
		}

	}

	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,
		rnaseq_zip=qualimapRNAseq.rnaseq_zip
	}

}