wgs_somatic_pipeline_v1/workflow.wdl

import "./tasks/fastp.wdl" as fastp
import "./tasks/fastqTobam.wdl" as fastqTobam
import "./tasks/qualimap.wdl" as qualimap
import "./tasks/BQSR.wdl" as Sentieon_BQSR
import "./tasks/TNseq.wdl" as TNseq
import "./tasks/TNscope.wdl" as TNscope
import "./tasks/manta.wdl" as manta_calling
import "./tasks/strelka.wdl" as strelka_calling


workflow {{ project_name }} {
	#sample info
    File? normal_in1
    File? normal_in2
	File? tumor_in1
	File? tumor_in2
    String sample_id
	String Seq_platform
	#reference fasta
	String ref_fasta
	File ref_fasta_dir
	File annot_gff
    File dbsnp_dir
    File dbmills_dir
    String dbsnp
    String db_mills
    File? regions
    Int? interval_padding
	File germline_resource
	File germline_resource_tbi

	#docker
    String docker_fastp
	String docker_sentieon
	String SENTIEON_LICENSE
	String docker_qualimap
	String docker_manta
	String docker_strelka

	#config
    String cluster_config
    String disk_size
	Boolean fastqc=false
	Boolean bamqc=false


if (normal_in1 != ""){
	
	if (fastqc){
		call fastp.fastp as fastp_normal{
			input:
				in1=normal_in1,
				in2=normal_in2,
				sample_id=sample_id+'_N',
				docker=docker_fastp,
				cluster_config=cluster_config,
				disk_size=disk_size	
	
	} 

	if (!fastqc){
		call fastqTobam.SentieonFastqToBam as SentieonFastqToBam_normal{
			input:
				fastq1=normal_in1,
				fastq2=normal_in2,
				sample_id=sample_id+'_N',
				Seq_platform=Seq_platform,
				ref_fasta=ref_fasta,
				ref_fasta_dir=ref_fasta_dir,
				SENTIEON_LICENSE=SENTIEON_LICENSE,
				docker=docker_sentieon,
				cluster_config=cluster_config,
				disk_size=disk_size

		}

		if (bamqc){
			call qualimap.qualimap as qualimap_normal{
				 input:
				 sample_id=sample_id+'_N',
				 bam_file=SentieonFastqToBam_normal.deduped_bam,
				 bam_bai=SentieonFastqToBam_normal.deduped_bam_bai,
				 annot_gff=annot_gff,
				 docker=docker_qualimap,
				 cluster_config=cluster_config,
				 disk_size=disk_size
			}


		}

		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_normal{
			input:
				ref_dir=ref_fasta_dir,
				dbsnp_dir=dbsnp_dir,
				dbmills_dir = dbmills_dir,
				sample_id=sample_id+'_N',
				ref_fasta=ref_fasta,
				dbsnp=dbsnp,
				db_mills=db_mills,
				deduped_bam=SentieonFastqToBam_normal.deduped_bam,
				deduped_bam_index=SentieonFastqToBam_normal.deduped_bam_bai,
				regions=regions,
				interval_padding=interval_padding,
				docker=docker_sentieon,
				cluster_config=cluster_config,
				disk_size=disk_size,
				SENTIEON_LICENSE=SENTIEON_LICENSE
		}

	}
	}

}

if (tumor_in1 != ""){
	
	if (fastqc){
		call fastp.fastp as fastp_tumor{
			input:
				in1=tumor_in1,
				in2=tumor_in2,
				sample_id=sample_id+'_T',
				docker=docker_fastp,
				cluster_config=cluster_config,
				disk_size=disk_size	
	
	} 

	if (!fastqc){
		call fastqTobam.SentieonFastqToBam as SentieonFastqToBam_tumor{
			input:
				fastq1=tumor_in1,
				fastq2=tumor_in2,
				sample_id=sample_id+'_T',
				Seq_platform=Seq_platform,
				ref_fasta=ref_fasta,
				ref_fasta_dir=ref_fasta_dir,
				SENTIEON_LICENSE=SENTIEON_LICENSE,
				docker=docker_sentieon,
				cluster_config=cluster_config,
				disk_size=disk_size

		}

		if (bamqc){
			call qualimap.qualimap as qualimap_tumor{
				 input:
				 sample_id=sample_id+'_T',
				 bam_file=SentieonFastqToBam_tumor.deduped_bam,
				 bam_bai=SentieonFastqToBam_tumor.deduped_bam_bai,
				 annot_gff=annot_gff,
				 docker=docker_qualimap,
				 cluster_config=cluster_config,
				 disk_size=disk_size
			}


		}

		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_tumor{
			input:
				ref_dir=ref_fasta_dir,
				dbsnp_dir=dbsnp_dir,
				dbmills_dir = dbmills_dir,
				sample_id=sample_id+'_T',
				ref_fasta=ref_fasta,
				dbsnp=dbsnp,
				db_mills=db_mills,
				deduped_bam=SentieonFastqToBam_normal.deduped_bam,
				deduped_bam_index=SentieonFastqToBam_normal.deduped_bam_bai,
				regions=regions,
				interval_padding=interval_padding,
				docker=docker_sentieon,
				cluster_config=cluster_config,
				disk_size=disk_size,
				SENTIEON_LICENSE=SENTIEON_LICENSE
		}

	}
	}

}

call TNseq.sentieon_TNseq as sentieon_TNseq{
	input:
		sample_id = sample_id,
		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
		normal_bam = Sentieon_BQSR_normal.recaled_bam,
		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
		tumor_name = sample_id+'_T',
		normal_name = sample_id+'_N',

		ref_dir = ref_fasta_dir,
		ref_fasta = ref_fasta,
		germline_resource = germline_resource,
		germline_resource_tbi = germline_resource_tbi,

		docker = docker_sentieon,
		cluster_config = cluster_config,
		disk_size = disk_size,
		SENTIEON_LICENSE = SENTIEON_LICENSE
}

call TNscope.sentieon_TNscope as sentieon_TNscope{
	input:
		sample_id = sample_id,
		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
		normal_bam = Sentieon_BQSR_normal.recaled_bam,
		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
		tumor_name = sample_id+'_T',
		normal_name = sample_id+'_N',
		tumor_recall_data = Sentieon_BQSR_normal.recaled_bam,
		normal_recall_data = Sentieon_BQSR_normal.recaled_bam_index,

		ref_dir = ref_fasta_dir,
		ref_fasta = ref_fasta,
		regions = regions,
		interval_padding = interval_padding,
		dbsnp_dir = dbsnp_dir,
		dbsnp = dbsnp,
		# excute env
		docker = docker_sentieon,
		cluster_config = cluster_config,
		disk_size = disk_size,
		SENTIEON_LICENSE = SENTIEON_LICENSE
}

call manta_calling.manta_calling as manta_calling{
	input:
		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
		normal_bam = Sentieon_BQSR_normal.recaled_bam,
		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
		ref_fasta = ref_fasta,
		ref_dir = ref_fasta_dir,
		sample_id = sample_id,
		docker = docker_manta,
		cluster_config = cluster_config,
		disk_size = disk_size

}

call strelka_calling.strelka_calling as strelka_calling{
	input:
		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
		normal_bam = Sentieon_BQSR_normal.recaled_bam,
		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
		ref_fasta = ref_fasta,
		ref_dir = ref_fasta_dir,
		sample_id = sample_id,
		manta_indel_vcf = manta_calling.manta_indel_vcf,
		manta_indel_vcf_index = manta_calling.manta_indel_vcf_index,
		
		docker=docker_strelka,
		cluster_config=cluster_config,
		disk_size=disk_size
}


}