更新 'workflow.wdl'

workflow.wdl

@@ -1,16 +1,3 @@
-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
@@ -33,6 +20,9 @@ workflow {{ project_name }} {
     File? regions
     File baseline
     File hg38_CDS
+    File tumor_recal_table
+    File normal_recal_table
+
 
 
 
@@ -57,49 +47,7 @@ workflow {{ project_name }} {
     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{
+call TNscope.sentieon_TNscope as sentieon_TNscope{
 	input:
 		sample_id = sample_id,
 		tumor_bam = tumor_deduped_bam,
@@ -108,23 +56,23 @@ call TNseq.sentieon_TNseq as sentieon_TNseq{
 		normal_bam_bai = normal_deduped_bam_bai,
 		tumor_name = sample_id+'_T',
 		normal_name = sample_id+'_N',
+		tumor_recall_data = tumor_recal_table,
+		normal_recall_data = normal_recal_table,
 
 		ref_dir = ref_fasta_dir,
 		ref_fasta = ref_fasta,
-		germline_resource = germline_resource,
-		germline_resource_tbi = germline_resource_tbi,
-
+		dbsnp_dir = dbsnp_dir,
+		dbsnp = dbsnp,
+		# excute env
 		docker = docker_sentieon,
 		cluster_config = cluster_config,
 		disk_size = disk_size,
 		SENTIEON_LICENSE = SENTIEON_LICENSE
 }
 
-
-
-call bcftools.bcftools as TNseq_bcftools {
+call bcftools.bcftools as TNscope_bcftools {
 	input:
-	vcf=sentieon_TNseq.vcf,
+	vcf=sentieon_TNscope.vcf,
 	fasta=ref_fasta,
 	ref_dir=ref_fasta_dir,
 	docker=docker_bcftools,
@@ -132,40 +80,80 @@ call bcftools.bcftools as TNseq_bcftools {
 	disk_size=disk_size
 }
 
+call manta_calling.manta_calling as manta_calling{
+	input:
+		tumor_bam = tumor_deduped_bam,
+		tumor_bam_bai = tumor_deduped_bam_bai,
+		normal_bam = normal_deduped_bam,
+		normal_bam_bai = normal_deduped_bam_bai,
+		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 = tumor_deduped_bam,
+		tumor_bam_bai = tumor_deduped_bam_bai,
+		normal_bam = normal_deduped_bam,
+		normal_bam_bai = normal_deduped_bam_bai,
+		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
+}
+
+call bcftools_concat.bcftools as bcftools_concat{
+        input:
+            ref_dir=ref_fasta_dir,
+            fasta=ref_fasta,
+            vcf_indels=strelka_calling.indel_vcf,
+            vcf_snvs=strelka_calling.snv_vcf,
+            sample_id=sample_id,
+            docker=docker_bcftools,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+
+    }
+
+call bcftools.bcftools as strelka_bcftools {
+	input:
+	vcf=bcftools_concat.concat_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 {
+
+  	call annovar.ANNOVAR as TNscope_ANNOVAR {
 		input:
-			vcf=TNseq_bcftools.norm_vcf,
+			vcf=TNscope_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
-  	# }
-
-
+    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
+  }
 
 }
 }