import "./tasks/mapping.wdl" as mapping
import "./tasks/Metrics.wdl" as Metrics
import "./tasks/Dedup.wdl" as Dedup
import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
import "./tasks/Realigner.wdl" as Realigner
import "./tasks/BQSR.wdl" as BQSR
import "./tasks/Haplotyper.wdl" as Haplotyper
import "./tasks/corealigner.wdl" as corealigner
import "./tasks/PON.wdl" as PON
import "./tasks/TNseq.wdl" as TNseq
import "./tasks/TNscope.wdl" as TNscope
import "./tasks/somatic.wdl" as somatic
import "./tasks/processSomatic.wdl" as processSomatic
import "./tasks/somaticFilter.wdl" as somaticFilter
import "./tasks/annovar.wdl" as annovar
import "./tasks/vcf2maf.wdl" as vcf2maf


workflow {{ project_name }} {
	
	String sample_id
	File tumor_fastq_1
	File tumor_fastq_2
	File normal_fastq_1
	File normal_fastq_2

	String SENTIEON_INSTALL_DIR
	String SENTIEON_LICENSE
	String sentieon_docker
	String annovar_docker
	String maftools_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 set_pon
	File? pon_vcf
	File? cosmic_dir
	String? cosmic_vcf

	Boolean germline
	Boolean TNseq
	Boolean TNscope
	Boolean Varscan


	call mapping.mapping as tumor_mapping {
		input: 
		group=sample_id + '_tumor',
		sample=sample_id + '_tumor',
		fastq_1=tumor_fastq_1,
		fastq_2=tumor_fastq_2,
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		pl="ILLUMINAL",
		fasta=fasta,
		ref_dir=ref_dir,
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call Metrics.Metrics as tumor_Metrics {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		sorted_bam=tumor_mapping.sorted_bam,
		sorted_bam_index=tumor_mapping.sorted_bam_index,
		sample=sample_id + '_tumor',
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call Dedup.Dedup as tumor_Dedup {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		sorted_bam=tumor_mapping.sorted_bam,
		sorted_bam_index=tumor_mapping.sorted_bam_index,
		sample=sample_id + '_tumor',
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call deduped_Metrics.deduped_Metrics as tumor_deduped_Metrics {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		Dedup_bam=tumor_Dedup.Dedup_bam,
		Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
		sample=sample_id + '_tumor',
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call Realigner.Realigner as tumor_Realigner {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		Dedup_bam=tumor_Dedup.Dedup_bam,
		Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		sample=sample_id + '_tumor',
		docker=sentieon_docker,
		disk_size=disk_size,
		regions=regions,
		cluster_config=cluster_config
	}

	call BQSR.BQSR as tumor_BQSR {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		realigned_bam=tumor_Realigner.realigner_bam,
		realigned_bam_index=tumor_Realigner.realigner_bam_index,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		sample=sample_id + '_tumor',
		regions=regions,
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call mapping.mapping as normal_mapping {
		input: 
		group=sample_id + '_normal',
		sample=sample_id + '_normal',
		fastq_1=normal_fastq_1,
		fastq_2=normal_fastq_2,
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		pl="ILLUMINAL",
		fasta=fasta,
		ref_dir=ref_dir,
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call Metrics.Metrics as normal_Metrics {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		sorted_bam=normal_mapping.sorted_bam,
		sorted_bam_index=normal_mapping.sorted_bam_index,
		sample=sample_id + '_normal',
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call Dedup.Dedup as normal_Dedup {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		sorted_bam=normal_mapping.sorted_bam,
		sorted_bam_index=normal_mapping.sorted_bam_index,
		sample=sample_id + '_normal',
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		Dedup_bam=normal_Dedup.Dedup_bam,
		Dedup_bam_index=normal_Dedup.Dedup_bam_index,
		sample=sample_id + '_normal',
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call Realigner.Realigner as normal_Realigner {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		Dedup_bam=normal_Dedup.Dedup_bam,
		Dedup_bam_index=normal_Dedup.Dedup_bam_index,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		sample=sample_id + '_normal',
		docker=sentieon_docker,
		disk_size=disk_size,
		regions=regions,
		cluster_config=cluster_config
	}

	call BQSR.BQSR as normal_BQSR {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		realigned_bam=normal_Realigner.realigner_bam,
		realigned_bam_index=normal_Realigner.realigner_bam_index,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		sample=sample_id + '_normal',
		regions=regions,
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	if (germline) {
		call Haplotyper.Haplotyper as Haplotyper {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			sample=sample_id + '_normal',
			fasta=fasta,
			ref_dir=ref_dir,
			recaled_bam=normal_BQSR.recaled_bam,
			recaled_bam_index=normal_BQSR.recaled_bam_index,
			dbsnp=dbsnp,
			dbsnp_dir=dbsnp_dir,
			regions=regions,
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}
	}
	
	call corealigner.corealigner as corealigner {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		sample=sample_id,
		docker=sentieon_docker,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		tumor_recaled_bam=tumor_BQSR.recaled_bam,
		tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
		normal_recaled_bam=normal_BQSR.recaled_bam,
		normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
		disk_size=disk_size,
		cluster_config=cluster_config
	}
	
	if (TNseq) {
		call TNseq.TNseq as TNseq {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			regions=regions,
			corealigner_bam=corealigner.corealigner_bam,
			corealigner_bam_index=corealigner.corealigner_bam_index,
			dbsnp=dbsnp,
			dbsnp_dir=dbsnp_dir,
			set_pon=set_pon,
			pon_vcf=pon_vcf,
			cosmic_vcf=cosmic_vcf,
			cosmic_dir=cosmic_dir,
			tumor_name=sample_id + "_tumor",
			normal_name=sample_id + "_normal",
			docker=sentieon_docker,
			sample=sample_id,
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call annovar.annovar as TNseq_annovar {
			input:
			sample=sample_id,
			vcf=TNseq.TNseq_vcf,
			database=database,
			docker=annovar_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}

		call vcf2maf.vcf2maf as TNseq_vcf2maf {
			input:
			sample=sample_id,
			multianno_txt=TNseq_annovar.multianno_txt,
			docker=maftools_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
	}

	if (TNscope) {
		call TNscope.TNscope as TNscope {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			regions=regions,
			corealigner_bam=corealigner.corealigner_bam,
			corealigner_bam_index=corealigner.corealigner_bam_index,
			dbsnp=dbsnp,
			dbsnp_dir=dbsnp_dir,
			set_pon=set_pon,
			pon_vcf=pon_vcf,
			cosmic_vcf=cosmic_vcf,
			cosmic_dir=cosmic_dir,
			tumor_name=sample_id + "_tumor",
			normal_name=sample_id + "_normal",
			docker=sentieon_docker,
			sample=sample_id,
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call annovar.annovar as TNscope_annovar {
			input:
			sample=sample_id,
			vcf=TNscope.TNscope_vcf,
			database=database,
			docker=annovar_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}

		call vcf2maf.vcf2maf as TNscope_vcf2maf {
			input:
			sample=sample_id,
			multianno_txt=TNscope_annovar.multianno_txt,
			docker=maftools_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
	}

	if (Varscan) {
		call somatic.somatic as somatic {
			input:
			sample=sample_id,
			tumor_bam=tumor_BQSR.recaled_bam,
			tumor_bam_index=tumor_BQSR.recaled_bam_index,
			normal_bam=normal_BQSR.recaled_bam,
			normal_bam_index=normal_BQSR.recaled_bam_index,
			ref_dir=ref_dir,
			fasta=fasta,        
			docker=varscan_docker,	
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call processSomatic.processSomatic as processSomatic {
			input:
			sample=sample_id,
			varscan_snp=somatic.varscan_snp,
			varscan_indel=somatic.varscan_indel,     
			docker=varscan_docker,	
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call somaticFilter.somaticFilter as somaticFilter {
			input:
			sample=sample_id,
			varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,
			varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,
			varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,
			varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,
			varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,
			varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,
			varscan_indel=somatic.varscan_indel,   
			docker=varscan_docker,	
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call annovar.annovar as snp_somatic_annovar {
			input: 
			sample=sample_id,
			vcf=somaticFilter.varscan_snp_somatic_filter,
			database=database,
			docker=annovar_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}

		call vcf2maf.vcf2maf as snp_somatic_vcf2maf {
			input:
			sample=sample_id,
			multianno_txt=snp_somatic_annovar.multianno_txt,
			docker=maftools_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		
		call annovar.annovar as snp_loh_annovar {
			input: 
			sample=sample_id,
			vcf=somaticFilter.varscan_snp_loh_filter,
			database=database,
			docker=annovar_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}

		call vcf2maf.vcf2maf as snp_loh_vcf2maf {
			input:
			sample=sample_id,
			multianno_txt=snp_loh_annovar.multianno_txt,
			docker=maftools_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		
		call annovar.annovar as indel_somatic_annovar {
			input: 
			sample=sample_id,
			vcf=somaticFilter.varscan_indel_somatic_filter,
			database=database,
			docker=annovar_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		
		call vcf2maf.vcf2maf as indel_somatic_vcf2maf {
			input:
			sample=sample_id,
			multianno_txt=indel_somatic_annovar.multianno_txt,
			docker=maftools_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		
		call annovar.annovar as indel_loh_annovar {
			input: 
			sample=sample_id,
			vcf=somaticFilter.varscan_indel_loh_filter,
			database=database,
			docker=annovar_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}

		call vcf2maf.vcf2maf as indel_loh_vcf2maf {
			input:
			sample=sample_id,
			multianno_txt=indel_loh_annovar.multianno_txt,
			docker=maftools_docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
	}
}