更新 'workflow.wdl'

workflow_raw.wdl → workflow.wdl

@@ -5,7 +5,9 @@ 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
 
 
 workflow {{ project_name }} {
@@ -27,6 +29,11 @@ workflow {{ project_name }} {
 	File germline_resource
 	File germline_resource_tbi
 	File annovar_database
+    File? regions
+    File baseline
+    File hg38_CDS
+
+
 
 	#docker
     String docker_fastp
@@ -37,6 +44,8 @@ workflow {{ project_name }} {
 	String docker_strelka
 	String docker_bcftools
 	String docker_annovar
+    String docker_tmb
+    String docker_tmb_MSIsensor
 
 	#config
     String cluster_config
@@ -44,6 +53,7 @@ workflow {{ project_name }} {
 	Boolean? fastqc
 	Boolean bamqc
 	Boolean Annovar
+    Boolean AF_filter
 
 
 if (normal_deduped_bam != ""){
@@ -88,6 +98,48 @@ 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=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=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=cluster_config,
+        disk_size=disk_size
+    }
+
 call TNseq.sentieon_TNseq as sentieon_TNseq{
 	input:
 		sample_id = sample_id,
@@ -109,6 +161,8 @@ call TNseq.sentieon_TNseq as sentieon_TNseq{
 		SENTIEON_LICENSE = SENTIEON_LICENSE
 }
 
+
+
 call bcftools.bcftools as TNseq_bcftools {
 	input:
 	vcf=sentieon_TNseq.vcf,
@@ -217,6 +271,18 @@ if (Annovar){
 			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 TNscope_ANNOVAR {
 		input:
 			vcf=TNscope_bcftools.norm_vcf,
@@ -226,14 +292,25 @@ if (Annovar){
 			disk_size=disk_size
   }
 
-    call annovar.ANNOVAR as strelka_ANNOVAR {
+    call annovar.ANNOVAR as Haplotyper_ANNOVAR {
 		input:
-			vcf=strelka_bcftools.norm_vcf,
+			vcf=Haplotyper_bcftools.norm_vcf,
 			annovar_database=annovar_database,
 			docker=docker_annovar,
 			cluster_config=cluster_config,
 			disk_size=disk_size
   }
+
+
+
+#     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
+#   }
 }
 
 }