wgs_somatic_pipeline_v1/workflow.wdl

#Only for BamQC
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 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
	Boolean bamqc


if (normal_in1 != ""){
	
		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

		}

		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
			}


	}

if (tumor_in1 != ""){

		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

		}

		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
			}



	}


}