first commit

inputs

   "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
-  "{{ project_name }}.pon_vcf1": "oss://share-data-temp/TNBC/vcf/FUSCCTNBC083_pon.vcf",
-  "{{ project_name }}.pon_vcf2": "oss://share-data-temp/TNBC/vcf/FUSCCTNBC330_pon.vcf",
-  "{{ project_name }}.pon_vcf3": "oss://share-data-temp/TNBC/vcf/FUSCCTNBC467_pon.vcf",
+  "{{ project_name }}.bcf": ["oss://share-data-temp/TNBC/vcf/FUSCCTNBC083_pon.vcf","oss://share-data-temp/TNBC/vcf/FUSCCTNBC330_pon.vcf","oss://share-data-temp/TNBC/vcf/FUSCCTNBC467_pon.vcf"],
   "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.PONmode": "{{ PONmode }}",
   "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",
   "{{ project_name }}.set_annovar": "{{ set_annovar }}",
   "{{ project_name }}.set_vcf2maf": "{{ set_vcf2maf }}"
 }
+

tasks/bcftools.wdl

 task bcftools {
 
-	File pon_vcf1
-	File pon_vcf2
-	File pon_vcf3
+	#File pon_vcf1
+	#File pon_vcf2
+	#File pon_vcf3
+	File bcfpon
 	String docker
 	String cluster_config
 	String disk_size
 		set -e
 		
 		if [ ${PONmode} ]; then
+			bcftools view ${bcfpon} -Oz -o $(basename ${bcfpon}.gz)
 			#mkdir -p /cromwell_root/tmp/bcftools
 			#bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			#bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			#bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			#cd /cromwell_root/tmp/bcftools
-			bcftools view ${pon_vcf1} -Oz -o $(basename ${pon_vcf1}.gz)
-			bcftools view ${pon_vcf2} -Oz -o $(basename ${pon_vcf2}.gz)
-			bcftools view ${pon_vcf2} -Oz -o $(basename ${pon_vcf3}.gz)
+			#bcftools view ${pon_vcf1} -Oz -o $(basename ${pon_vcf1}.gz)
+			#bcftools view ${pon_vcf2} -Oz -o $(basename ${pon_vcf2}.gz)
+			#bcftools view ${pon_vcf2} -Oz -o $(basename ${pon_vcf3}.gz)
 			#for i in `ls *.gz`; do bcftools index $i -f; done
 			#bcftools merge -m all -f PASS,. --force-samples *.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
 		else
 	}
 	
 	output {
-		File vcf1="$(basename ${pon_vcf1}.gz)"
-		File vcf2="$(basename ${pon_vcf2}.gz)"
-		File vcf3="$(basename ${pon_vcf3}.gz)"
+		File vcf1="$(basename ${bcfpon}.gz)"
+		#File vcf1="$(basename ${pon_vcf1}.gz)"
+		#File vcf2="$(basename ${pon_vcf2}.gz)"
+		#File vcf3="$(basename ${pon_vcf3}.gz)"
 		#File panel_of_normal_vcf = "panel_of_normal.vcf"
 	}
 }

workflow.wdl

 	Boolean set_vcf2maf
 
 
-	File pon_vcf1
-	File pon_vcf2
-	File pon_vcf3
-	#Array[Array[File]] bcf = read_tsv(inputponfile)
-
-	call bcftools.bcftools as bcftools {
-		input:
-		PONmode=PONmode,
-		pon_vcf1=pon_vcf1,
-		pon_vcf2=pon_vcf2,
-		pon_vcf3=pon_vcf3,
-		docker=bcftools_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
-	
-	
-	scatter (sample in inputSamples) {
-		call corealigner.corealigner as corealigner {
-	        input:
-    	    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    	    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    	    fasta=fasta,
-    	    ref_dir=ref_dir,
-       		sample=sample[0],
-    	    docker=sentieon_docker,
-        	db_mills=db_mills,
-	        dbmills_dir=dbmills_dir,
-    	    dbsnp=dbsnp,
-        	dbsnp_dir=dbsnp_dir,
-	        tumor_recaled_bam=sample[1],
-    	    tumor_recaled_bam_index=sample[2],
-        	normal_recaled_bam=sample[3],
-	        normal_recaled_bam_index=sample[4],
-    	    disk_size=disk_size,
-        	cluster_config=cluster_config
-    	}
-
-    	call TNseq.TNseq as TNseq {
-            input:
-            SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-            SENTIEON_LICENSE=SENTIEON_LICENSE,
-            PONmode=PONmode,
-            fasta=fasta,
-            ref_dir=ref_dir,
-            corealigner_bam=corealigner.corealigner_bam,
-            corealigner_bam_index=corealigner.corealigner_bam_index,
-            dbsnp=dbsnp,
-            dbsnp_dir=dbsnp_dir,
-            tumor_name=sample[0] + "_tumor",
-            normal_name=sample[0] + "_normal",
-            cosmic_vcf=cosmic_vcf,
-            cosmic_dir=cosmic_dir,
-            #panel_of_normal_vcf = bcftools.panel_of_normal_vcf,
-            docker=sentieon_docker,
-            sample=sample[0],
-            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.corealigner_bam,
-            corealigner_bam_index=corealigner.corealigner_bam_index,
-            dbsnp=dbsnp,
-            dbsnp_dir=dbsnp_dir,
-            tumor_name=sample[0] + "_tumor",
-            normal_name=sample[0] + "_normal",
-            cosmic_vcf=cosmic_vcf,
-            cosmic_dir=cosmic_dir,
-            #panel_of_normal_vcf = bcftools.panel_of_normal_vcf,
-            docker=sentieon_docker,
-            sample=sample[0],
-            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[0],
-                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[0],
-                cluster_config=cluster_config,
-                disk_size=disk_size
-            }
-        }
+	#File pon_vcf1
+	#File pon_vcf2
+	#File pon_vcf3
+	Array[File] bcf
+
+	scatter (sample in bcf) {
+		call bcftools.bcftools as bcftools {
+			input:
+			PONmode=PONmode,
+			bcfpon=sample,
+			#pon_vcf1=pon_vcf1,
+			#pon_vcf2=pon_vcf2,
+			#pon_vcf3=pon_vcf3,
+			docker=bcftools_docker,
+			disk_size=disk_size,
+			cluster_config=cluster_config
+		}
 	}
-}
+}