first commit

inputs

 {
-
+  "{{ project_name }}.vcf": "{{ vcf }}",
+  "{{ project_name }}.sample": "{{ sample }}",
   "{{ project_name }}.picard_docker": "{{ picard_docker }}",
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}",
   "{{ project_name }}.chain_dir": "{{ chain_dir }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}"
-}
+}

tasks/picard.wdl

-task annovar {
+task picard {
 
 	File vcf
 	String sample
+	File ref_dir
+	String fasta
+	File chain_dir
+	String chain
 	String docker
 	String cluster_config
 	String disk_size
 
-
 	command <<<
 		set -o pipefail
 		set -e

workflow.wdl

-import "./tasks/PON.wdl" as PON
-import "./tasks/bcftools.wdl" as bcftools
-import "./tasks/TNseq.wdl" as TNseq
-import "./tasks/TNscope.wdl" as TNscope
-import "./tasks/annovar.wdl" as annovar
-import "./tasks/vcf2maf.wdl" as vcf2maf
-
+import "./tasks/picard.wdl" as picard
 
 workflow {{ project_name }} {
 
-	File normal_recaled_bam
-	File normal_recaled_bam_index
-	File corealigner_bam
-	File corealigner_bam_index
-
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
+	File vcf
 	String sample
-	String sentieon_docker
-	String annovar_docker
-	String vcf2maf_r_docker
-	String bcftools_docker
-	
 	File ref_dir
 	String fasta
-	File dbmills_dir
-	String db_mills
-	File dbsnp_dir
-	String dbsnp
-	File regions
-	File database
-	String disk_size
+	File chain_dir
+	String chain
+	String picard_docker
 	String cluster_config
+	String disk_size
 
-	Boolean PONmode
-	File? cosmic_dir
-	String? cosmic_vcf
-
-	Boolean set_annovar
-	Boolean set_vcf2maf
-
-
-	if (PONmode) {
-		call PON.PON as PON {
-			input:
-			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			sample=sample,
-			fasta=fasta,
-			ref_dir=ref_dir,
-			normal_recaled_bam=normal_recaled_bam,
-			normal_recaled_bam_index=normal_recaled_bam_index,
-			cosmic_vcf=cosmic_vcf,
-			cosmic_dir=cosmic_dir,
-			dbsnp=dbsnp,
-			dbsnp_dir=dbsnp_dir,
-			docker=sentieon_docker,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
-		call bcftools.bcftools as bcftools {
-			input:
-			pon_vcf=PON.pon_vcf,
-			docker=bcftools_docker,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
-	}
-
-
-	call TNseq.TNseq as TNseq {
+	call picard.picard as picard {
 		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		PONmode=PONmode,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		corealigner_bam=corealigner_bam,
-		corealigner_bam_index=corealigner_bam_index,
-		dbsnp=dbsnp,
-		dbsnp_dir=dbsnp_dir,
-		tumor_name=sample + "tumor",
-		normal_name=sample + "normal",
-		cosmic_vcf=cosmic_vcf,
-		cosmic_dir=cosmic_dir,
-		panel_of_normal_vcf = bcftools.panel_of_normal_vcf,
-		docker=sentieon_docker,
+		vcf=vcf,
 		sample=sample,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
-    
-	call TNscope.TNscope as TNscope {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		PONmode=PONmode,
-		fasta=fasta,
 		ref_dir=ref_dir,
-		corealigner_bam=corealigner_bam,
-		corealigner_bam_index=corealigner_bam_index,
-		dbsnp=dbsnp,
-		dbsnp_dir=dbsnp_dir,
-		tumor_name=sample + "tumor",
-		normal_name=sample + "normal",
-		cosmic_vcf=cosmic_vcf,
-		cosmic_dir=cosmic_dir,
-		panel_of_normal_vcf = bcftools.panel_of_normal_vcf,
-		docker=sentieon_docker,
-		sample=sample,
+		fasta=fasta,
+		chain_dir=chain_dir,
+		chain=chain,
+		docker=picard_docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
-
-	if (set_annovar){
-		call annovar.annovar as annovar {
-			input:
-			docker=annovar_docker,
-			database=database,
-			tnscope_vcf_file=TNscope.TNscope_vcf,
-			tnseq_vcf_file=TNseq.TNseq_vcf,
-			sample=sample,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-	}
-	
-	if (set_vcf2maf){
-		call vcf2maf.vcf2maf as vcf2maf {
-			input:
-			docker=vcf2maf_r_docker,
-			multianno_tnscope_txt=annovar.multianno_tnscope_txt,
-			multianno_tnseq_txt=annovar.multianno_tnseq_txt,
-			sample=sample,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-	}
 }