TNScope_and_Stralka/workflow.wdl

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
import "./tasks/bcftools.wdl" as bcftools
import "./tasks/bcftools_concat.wdl" as bcftools_concat
import "./tasks/annovar.wdl" as annovar
import "./tasks/Haplotyper.wdl" as Haplotyper
import "./tasks/MSIsensor.wdl" as MSIsensor
import "./tasks/tmb.wdl" as tmb

#VIP客户（只用TNseq进行call）
workflow {{ project_name }} {
	#sample info
    File? normal_deduped_bam
    File? normal_deduped_bam_bai
	File? tumor_deduped_bam
	File? tumor_deduped_bam_bai
    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
	File annovar_database
    File? regions
    File baseline
    File hg38_CDS



	#docker
    String docker_fastp
	String docker_sentieon
	String SENTIEON_LICENSE
	String docker_qualimap
	String docker_manta
	String docker_strelka
	String docker_bcftools
	String docker_annovar
    String docker_tmb
    String docker_MSIsensor

	#config
    String cluster_config
    String disk_size
	Boolean? fastqc
	Boolean bamqc
	Boolean Annovar
    Boolean AF_filter


# call MSIsensor.MSIsensor as MSIsensor {
#     input:
#     sample=sample_id,
#     fasta=ref_fasta,
#     ref_dir=ref_fasta_dir,
#     normal_bam=normal_deduped_bam,
#     normal_bam_index=normal_deduped_bam_bai,
#     tumor_bam=tumor_deduped_bam,
#     tumor_bam_index=tumor_deduped_bam_bai,
#     baseline=baseline,
#     docker=docker_MSIsensor,
#     cluster_config=cluster_config,
#     disk_size=disk_size
#   }


# call Haplotyper.Haplotyper as Haplotyper {
#       input:
#         SENTIEON_LICENSE=SENTIEON_LICENSE,
#         sample=sample_id + '.N',
#         fasta=ref_fasta,
#         ref_dir=ref_fasta_dir,
#         recaled_bam=normal_deduped_bam,
#         recaled_bam_index=normal_deduped_bam_bai,
#         dbsnp=dbsnp,
#         dbsnp_dir=dbsnp_dir,
#         regions=regions,
#         docker=docker_sentieon,
#         disk_size=disk_size,
#         cluster_config=cluster_config
#     }

# call bcftools.bcftools as Haplotyper_bcftools {
#       input:
#         vcf=Haplotyper.vcf,
#         fasta=ref_fasta,
#         ref_dir=ref_fasta_dir,
#         docker=docker_bcftools,
#         cluster_config=cluster_config,
#         disk_size=disk_size
#     }

call TNseq.sentieon_TNseq as sentieon_TNseq{
	input:
		sample_id = sample_id,
		tumor_bam = tumor_deduped_bam,
		tumor_bam_bai = tumor_deduped_bam_bai,
		normal_bam = normal_deduped_bam,
		normal_bam_bai = normal_deduped_bam_bai,
		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 bcftools.bcftools as TNseq_bcftools {
	input:
	vcf=sentieon_TNseq.vcf,
	fasta=ref_fasta,
	ref_dir=ref_fasta_dir,
	docker=docker_bcftools,
	cluster_config=cluster_config,
	disk_size=disk_size
}



if (Annovar){
	call annovar.ANNOVAR as TNseq_ANNOVAR {
		input:
			vcf=TNseq_bcftools.norm_vcf,
			annovar_database=annovar_database,
			docker=docker_annovar,
			cluster_config=cluster_config,
			disk_size=disk_size
  }

    # call tmb.TMB as TMB{
    #     input:
    #         sample=sample_id,
    #         hg38_CDS=hg38_CDS,
    #         regions=regions,
    #         snpindel_txt=TNseq_ANNOVAR.multianno_txt,
    #         docker=docker_tmb,
    #         cluster_config=cluster_config,
    #         disk_size=disk_size,
    #         AF_filter=AF_filter
    # }

    # call annovar.ANNOVAR as Haplotyper_ANNOVAR {
	# 	input:
	# 		vcf=Haplotyper_bcftools.norm_vcf,
	# 		annovar_database=annovar_database,
	# 		docker=docker_annovar,
	# 		cluster_config=cluster_config,
	# 		disk_size=disk_size
  	# }



}
}