Update: Add ANNOVAR

workflow.wdl

@@ -3,119 +3,119 @@ import "./tasks/TNscope.wdl" as TNscope
 import "./tasks/annovar.wdl" as annovar
 
 workflow {{ project_name }} {
-    
-    String sample_id
-    File tumor_bam
-    File tumor_bai
-    File tumor_table
-    File normal_bam
-    File normal_bai
-    File normal_table
+  
+  String sample_id
+  File tumor_bam
+  File tumor_bai
+  File tumor_table
+  File normal_bam
+  File normal_bai
+  File normal_table
 
-    String SENTIEON_INSTALL_DIR
-    String SENTIEON_LICENSE
-    String sentieon_docker
-    String varscan_docker
-    String annovar_docker
-    String maftools_docker
-    
-    File ref_dir
-    String fasta
-    File dbmills_dir
-    String db_mills
-    File dbsnp_dir
-    String dbsnp
-    File germline_resource
-    File germline_resource_tbi
-    
-    File? regions
-    Int? interval_padding
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  String sentieon_docker
+  String varscan_docker
+  String annovar_docker
+  String maftools_docker
+  
+  File ref_dir
+  String fasta
+  File dbmills_dir
+  String db_mills
+  File dbsnp_dir
+  String dbsnp
+  File germline_resource
+  File germline_resource_tbi
+  
+  File? regions
+  Int? interval_padding
 
-    File database
-    String disk_size
-    String cluster_config
+  File database
+  String disk_size
+  String cluster_config
 
-    File? tnseq_pon
-    File? tnscope_pon
-    File? cosmic_dir
-    String? cosmic_vcf
+  File? tnseq_pon
+  File? tnscope_pon
+  File? cosmic_dir
+  String? cosmic_vcf
 
-    Boolean germline
-    Boolean tnseq
-    Boolean tnscope
-    Boolean varscan
+  Boolean germline
+  Boolean tnseq
+  Boolean tnscope
+  Boolean varscan
 
-    if (tnseq) {
-        call TNseq.TNseq as TNseq {
-            input:
-            SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-            SENTIEON_LICENSE=SENTIEON_LICENSE,
-            sample=sample_id,
-            normal_recaled_bam=normal_bam,
-            normal_recaled_bam_index=normal_bai,
-            normal_recal_table=normal_table,
-            tumor_recaled_bam=tumor_bam,
-            tumor_recaled_bam_index=tumor_bai,
-            tumor_recal_table=tumor_table,
-            normal_name=sample_id + "_normal",
-            tumor_name=sample_id + "_tumor",
-            fasta=fasta,
-            ref_dir=ref_dir,
-            regions=regions,
-            interval_padding=interval_padding,
-            germline_resource=germline_resource,
-            germline_resource_tbi=germline_resource_tbi,
-            pon_vcf=tnseq_pon,
-            docker=sentieon_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
+  if (tnseq) {
+    call TNseq.TNseq as TNseq {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id,
+      normal_recaled_bam=normal_bam,
+      normal_recaled_bam_index=normal_bai,
+      normal_recal_table=normal_table,
+      tumor_recaled_bam=tumor_bam,
+      tumor_recaled_bam_index=tumor_bai,
+      tumor_recal_table=tumor_table,
+      normal_name=sample_id + "_normal",
+      tumor_name=sample_id + "_tumor",
+      fasta=fasta,
+      ref_dir=ref_dir,
+      regions=regions,
+      interval_padding=interval_padding,
+      germline_resource=germline_resource,
+      germline_resource_tbi=germline_resource_tbi,
+      pon_vcf=tnseq_pon,
+      docker=sentieon_docker,
+      cluster_config=cluster_config,
+      disk_size=disk_size
+    }
 
-        call annovar.annovar as TNseq_annovar {
-        input:
-            sample=sample_id,
-            vcf=TNseq.TNseq_vcf,
-            database=database,
-            docker=annovar_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
+    call annovar.annovar as TNseq_annovar {
+    input:
+      sample=sample_id,
+      vcf=TNseq.TNseq_vcf,
+      database=database,
+      docker=annovar_docker,
+      cluster_config=cluster_config,
+      disk_size=disk_size
     }
+  }
 
-    if (tnscope) {
-        call TNscope.TNscope as TNscope {
-            input:
-            SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-            SENTIEON_LICENSE=SENTIEON_LICENSE,
-            sample=sample_id,
-            normal_recaled_bam=normal_bam,
-            normal_recaled_bam_index=normal_bai,
-            normal_recal_table=normal_table,
-            tumor_recaled_bam=tumor_bam,
-            tumor_recaled_bam_index=tumor_bai,
-            tumor_recal_table=tumor_table,
-            normal_name=sample_id + "_normal",
-            tumor_name=sample_id + "_tumor",
-            fasta=fasta,
-            ref_dir=ref_dir,
-            regions=regions,
-            interval_padding=interval_padding,
-            dbsnp=dbsnp,
-            dbsnp_dir=dbsnp_dir,
-            pon_vcf=tnscope_pon,
-            docker=sentieon_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
+  if (tnscope) {
+    call TNscope.TNscope as TNscope {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id,
+      normal_recaled_bam=normal_bam,
+      normal_recaled_bam_index=normal_bai,
+      normal_recal_table=normal_table,
+      tumor_recaled_bam=tumor_bam,
+      tumor_recaled_bam_index=tumor_bai,
+      tumor_recal_table=tumor_table,
+      normal_name=sample_id + "_normal",
+      tumor_name=sample_id + "_tumor",
+      fasta=fasta,
+      ref_dir=ref_dir,
+      regions=regions,
+      interval_padding=interval_padding,
+      dbsnp=dbsnp,
+      dbsnp_dir=dbsnp_dir,
+      pon_vcf=tnscope_pon,
+      docker=sentieon_docker,
+      cluster_config=cluster_config,
+      disk_size=disk_size
+    }
 
-        call annovar.annovar as TNscope_annovar {
-            input:
-            sample=sample_id,
-            vcf=TNscope.TNscope_vcf,
-            database=database,
-            docker=annovar_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
+    call annovar.annovar as TNscope_annovar {
+      input:
+      sample=sample_id,
+      vcf=TNscope.TNscope_vcf,
+      database=database,
+      docker=annovar_docker,
+      cluster_config=cluster_config,
+      disk_size=disk_size
     }
+  }
 }