更新 'workflow_SEQC2.wdl'

workflow_SEQC2.wdl

@@ -1,4 +1,3 @@
-#import "./tasks/fastp.wdl" as fastp
 import "./tasks/BQSR.wdl" as Sentieon_BQSR
 import "./tasks/TNseq.wdl" as TNseq
 import "./tasks/TNscope.wdl" as TNscope
@@ -7,31 +6,36 @@ 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
 
 
-#如果是SEQC的结果，应该是'T_1'和'N_1'
 workflow {{ project_name }} {
 	#sample info
-    File? normal_deduped_bam
-    File? normal_deduped_bam_bai
+  File? normal_deduped_bam
+  File? normal_deduped_bam_bai
 	File? tumor_deduped_bam
 	File? tumor_deduped_bam_bai
-    String sample_id
+  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 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_fastp
 	String docker_sentieon
 	String SENTIEON_LICENSE
 	String docker_qualimap
@@ -39,15 +43,18 @@ workflow {{ project_name }} {
 	String docker_strelka
 	String docker_bcftools
 	String docker_annovar
+  String docker_tmb
+  String docker_MSIsensor
 
 	#config
-    String cluster_config
-    String disk_size
+  String cluster_config
+  String disk_size
 	Boolean? fastqc
 	Boolean bamqc
 	Boolean Annovar
+  Boolean AF_filter
 
-
+#SEQC2应该是_N_1和T_1
 if (normal_deduped_bam != ""){
 
 		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_normal{
@@ -90,6 +97,48 @@ if (tumor_deduped_bam != ""){
 
 	}
 
+call MSIsensor.MSIsensor as MSIsensor {
+    input:
+    sample=sample_id,
+    fasta=ref_fasta,
+    ref_dir=ref_fasta_dir,
+    normal_bam=Sentieon_BQSR_normal.recaled_bam,
+    normal_bam_index=Sentieon_BQSR_normal.recaled_bam_index,
+    tumor_bam=Sentieon_BQSR_tumor.recaled_bam,
+    tumor_bam_index=Sentieon_BQSR_tumor.recaled_bam_index,
+    baseline=baseline,
+    docker=docker_MSIsensor,
+    cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
+    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=Sentieon_BQSR_normal.recaled_bam,
+        recaled_bam_index=Sentieon_BQSR_normal.recaled_bam_index,
+        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="OnDemand bcs.ps.g.large img-ubuntu-vpc",
+        disk_size=disk_size
+    }
+
 call TNseq.sentieon_TNseq as sentieon_TNseq{
 	input:
 		sample_id = sample_id,
@@ -111,13 +160,15 @@ call TNseq.sentieon_TNseq as sentieon_TNseq{
 		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,
+	cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
 	disk_size=disk_size
 }
 
@@ -150,24 +201,10 @@ call bcftools.bcftools as TNscope_bcftools {
 	fasta=ref_fasta,
 	ref_dir=ref_fasta_dir,
 	docker=docker_bcftools,
-	cluster_config=cluster_config,
+	cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
 	disk_size=disk_size
 }
 
-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:
@@ -178,11 +215,9 @@ call strelka_calling.strelka_calling as strelka_calling{
 		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,
+		cluster_config="OnDemand bcs.ps.g.6xlarge img-ubuntu-vpc",
 		disk_size=disk_size
 }
 
@@ -194,48 +229,34 @@ call bcftools_concat.bcftools as bcftools_concat{
             vcf_snvs=strelka_calling.snv_vcf,
             sample_id=sample_id,
             docker=docker_bcftools,
-            cluster_config=cluster_config,
+            cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
             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 {
 		input:
 			vcf=TNseq_bcftools.norm_vcf,
 			annovar_database=annovar_database,
 			docker=docker_annovar,
-			cluster_config=cluster_config,
+			cluster_config="OnDemand bcs.ps.g.6xlarge img-ubuntu-vpc",
 			disk_size=disk_size
   }
 
-  	call annovar.ANNOVAR as TNscope_ANNOVAR {
-		input:
-			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="OnDemand bcs.ps.g.large img-ubuntu-vpc",
+            disk_size=disk_size,
+            AF_filter=AF_filter
+    }
+
 
-    call annovar.ANNOVAR as strelka_ANNOVAR {
-		input:
-			vcf=strelka_bcftools.norm_vcf,
-			annovar_database=annovar_database,
-			docker=docker_annovar,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-  }
 }
 
 }