import "./tasks/corealigner.wdl" as corealigner
import "./tasks/bcftools.wdl" as bcftools
import "./tasks/TNseq.wdl" as TNseq
import "./tasks/TNscope.wdl" as TNscope
import "./tasks/annovar.wdl" as annovar
import "./tasks/vcf2maf.wdl" as vcf2maf


workflow {{ project_name }} {

	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	#Array[String] sample

	String SENTIEON_INSTALL_DIR
	String SENTIEON_LICENSE
	String sentieon_docker
	String annovar_docker
	String vcf2maf_r_docker
	String bcftools_docker
	
	File ref_dir
	String fasta
	File dbmills_dir
	String db_mills
	File dbsnp_dir
	String dbsnp
	File regions
	File database
	String disk_size
	String cluster_config

	Boolean PONmode
	File? cosmic_dir
	String? cosmic_vcf

	Boolean set_annovar
	Boolean set_vcf2maf


	File inputponfile
	Array[Array[File]] bcf = read_tsv(inputponfile)

	call bcftools.bcftools as bcftools {
		input:
		PONmode=PONmode,
		pon_vcf=bcf,
		docker=bcftools_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}
	
	
	scatter (sample in inputSamples) {
		call corealigner.corealigner as corealigner {
	        input:
    	    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
    	    SENTIEON_LICENSE=SENTIEON_LICENSE,
    	    fasta=fasta,
    	    ref_dir=ref_dir,
       		sample=sample[0],
    	    docker=sentieon_docker,
        	db_mills=db_mills,
	        dbmills_dir=dbmills_dir,
    	    dbsnp=dbsnp,
        	dbsnp_dir=dbsnp_dir,
	        tumor_recaled_bam=sample[1],
    	    tumor_recaled_bam_index=sample[2],
        	normal_recaled_bam=sample[3],
	        normal_recaled_bam_index=sample[4],
    	    disk_size=disk_size,
        	cluster_config=cluster_config
    	}

    	call TNseq.TNseq as TNseq {
            input:
            SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
            SENTIEON_LICENSE=SENTIEON_LICENSE,
            PONmode=PONmode,
            fasta=fasta,
            ref_dir=ref_dir,
            corealigner_bam=corealigner.corealigner_bam,
            corealigner_bam_index=corealigner.corealigner_bam_index,
            dbsnp=dbsnp,
            dbsnp_dir=dbsnp_dir,
            tumor_name=sample[0] + "_tumor",
            normal_name=sample[0] + "_normal",
            cosmic_vcf=cosmic_vcf,
            cosmic_dir=cosmic_dir,
            panel_of_normal_vcf = bcftools.panel_of_normal_vcf,
            docker=sentieon_docker,
            sample=sample[0],
            disk_size=disk_size,
            cluster_config=cluster_config
        }
    
        call TNscope.TNscope as TNscope {
            input:
            SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
            SENTIEON_LICENSE=SENTIEON_LICENSE,
            PONmode=PONmode,
            fasta=fasta,
            ref_dir=ref_dir,
            corealigner_bam=corealigner.corealigner_bam,
            corealigner_bam_index=corealigner.corealigner_bam_index,
            dbsnp=dbsnp,
            dbsnp_dir=dbsnp_dir,
            tumor_name=sample[0] + "_tumor",
            normal_name=sample[0] + "_normal",
            cosmic_vcf=cosmic_vcf,
            cosmic_dir=cosmic_dir,
            panel_of_normal_vcf = bcftools.panel_of_normal_vcf,
            docker=sentieon_docker,
            sample=sample[0],
            disk_size=disk_size,
            cluster_config=cluster_config
        }

        if (set_annovar){
            call annovar.annovar as annovar {
                input:
                docker=annovar_docker,
                database=database,
                tnscope_vcf_file=TNscope.TNscope_vcf,
                tnseq_vcf_file=TNseq.TNseq_vcf,
                sample=sample[0],
                cluster_config=cluster_config,
                disk_size=disk_size
            }
        }
    
        if (set_vcf2maf){
            call vcf2maf.vcf2maf as vcf2maf {
                input:
                docker=vcf2maf_r_docker,
                multianno_tnscope_txt=annovar.multianno_tnscope_txt,
                multianno_tnseq_txt=annovar.multianno_tnseq_txt,
                sample=sample[0],
                cluster_config=cluster_config,
                disk_size=disk_size
            }
        }
	}
}