更新 'workflow.wdl'

workflow.wdl

@@ -13,31 +13,29 @@ import "./tasks/tmb.wdl" as tmb
 
 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
-
-
+  File? regions
+  File baseline
+  File hg38_CDS
 
 	#docker
-    String docker_fastp
+  String docker_fastp
 	String docker_sentieon
 	String SENTIEON_LICENSE
 	String docker_qualimap
@@ -45,16 +43,16 @@ workflow {{ project_name }} {
 	String docker_strelka
 	String docker_bcftools
 	String docker_annovar
-    String docker_tmb
-    String docker_MSIsensor
+  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
+  Boolean AF_filter
 
 
 if (normal_deduped_bam != ""){
@@ -110,7 +108,7 @@ call MSIsensor.MSIsensor as MSIsensor {
     tumor_bam_index=Sentieon_BQSR_tumor.recaled_bam_index,
     baseline=baseline,
     docker=docker_MSIsensor,
-    cluster_config=cluster_config,
+    cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
     disk_size=disk_size
   }
 
@@ -137,7 +135,7 @@ call bcftools.bcftools as Haplotyper_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
     }
 
@@ -170,7 +168,7 @@ call bcftools.bcftools as TNseq_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
 }
 
@@ -203,7 +201,7 @@ 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
 }
 
@@ -219,7 +217,7 @@ call strelka_calling.strelka_calling as strelka_calling{
 		sample_id = sample_id,
 		
 		docker=docker_strelka,
-		cluster_config=cluster_config,
+		cluster_config="OnDemand bcs.ps.g.6xlarge img-ubuntu-vpc",
 		disk_size=disk_size
 }
 
@@ -231,7 +229,7 @@ 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
 
     }
@@ -242,7 +240,7 @@ call bcftools.bcftools as strelka_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
 }
 
@@ -252,7 +250,7 @@ if (Annovar){
 			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
   }
 
@@ -263,39 +261,12 @@ if (Annovar){
             regions=regions,
             snpindel_txt=TNseq_ANNOVAR.multianno_txt,
             docker=docker_tmb,
-            cluster_config=cluster_config,
+            cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
             disk_size=disk_size,
             AF_filter=AF_filter
     }
 
-  	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 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 strelka_ANNOVAR {
-# 		input:
-# 			vcf=strelka_bcftools.norm_vcf,
-# 			annovar_database=annovar_database,
-# 			docker=docker_annovar,
-# 			cluster_config=cluster_config,
-# 			disk_size=disk_size
-#   }
 }
 
 }