remove -t

tasks/bcf2vcf.wdl

@@ -1,16 +1,7 @@
 task bcf2vcf {
 	
-	File ins_bcf
-	File ins_bcf_index
-	File del_bcf
-	File del_bcf_index
-	File dup_bcf
-	File dup_bcf_index
-	File inv_bcf
-	File inv_bcf_index
-	File bnd_bcf
-	File bnd_bcf_index
-
+	File bcf
+	File bcf_index
 	String sample_name
 	String docker
 	String disk_size
@@ -21,11 +12,7 @@ task bcf2vcf {
 
 		set -o pipefail
 		set -e
-		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${ins_bcf} > ${sample_name}.ins.vcf
-		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${del_bcf} > ${sample_name}.del.vcf
-		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${dup_bcf} > ${sample_name}.dup.vcf
-		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${inv_bcf} > ${sample_name}.inv.vcf
-		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${bnd_bcf} > ${sample_name}.bnd.vcf	
+		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${bcf} > ${sample_name}.vcf
 		>>>
 
 		runtime {
@@ -36,11 +23,7 @@ task bcf2vcf {
 	}
 
 	output {
-		File ins_vcf = "${sample_name}.ins.vcf"
-		File del_vcf = "${sample_name}.del.vcf"
-		File dup_vcf = "${sample_name}.dup.vcf"
-		File inv_vcf = "${sample_name}.inv.vcf"
-		File bnd_vcf = "${sample_name}.bnd.vcf"
+		File ins_vcf = "${sample_name}.vcf"
 	}
 }
 

tasks/delly.wdl

@@ -20,25 +20,10 @@ task delly {
 		nt=$(nproc)
 		export OMP_NUM_THREADS=$nt
 
-		/opt/delly/src/delly call -t DEL -g ${ref_dir}/${fasta} -o ${sample_name}.delly.del.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
+		/opt/delly/src/delly call -g ${ref_dir}/${fasta} -o ${sample_name}.delly.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
 
-		/opt/delly/src/delly filter -t DEL -f somatic -o ${sample_name}.delly.del.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.del.somatic.bcf
+		/opt/delly/src/delly filter -f somatic -o ${sample_name}.delly.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.somatic.bcf
 
-		/opt/delly/src/delly call -t DUP -g ${ref_dir}/${fasta} -o ${sample_name}.delly.dup.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
-
-		/opt/delly/src/delly filter -t DUP -f somatic -o ${sample_name}.delly.dup.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.dup.somatic.bcf
-
-		/opt/delly/src/delly call -t INS -g ${ref_dir}/${fasta} -o ${sample_name}.delly.ins.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
-
-		/opt/delly/src/delly filter -t INS -f somatic -o ${sample_name}.delly.ins.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.ins.somatic.bcf
-
-		/opt/delly/src/delly call -t INV -g ${ref_dir}/${fasta} -o ${sample_name}.delly.inv.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
-
-		/opt/delly/src/delly filter -t INV -f somatic -o ${sample_name}.delly.inv.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.inv.somatic.bcf
-
-		/opt/delly/src/delly call -t BND -g ${ref_dir}/${fasta} -o ${sample_name}.delly.bnd.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
-
-		/opt/delly/src/delly filter -t BND -f somatic -o ${sample_name}.delly.bnd.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.bnd.somatic.bcf
 
 		>>>
 
@@ -50,16 +35,8 @@ task delly {
 	}
 
 	output {
-		File del_bcf = "${sample_name}.delly.del.somatic.filtered.bcf"
-		File del_bcf_index = "${sample_name}.delly.del.somatic.filtered.bcf.csi"
-		File dup_bcf = "${sample_name}.delly.dup.somatic.filtered.bcf"
-		File dup_bcf_index = "${sample_name}.delly.dup.somatic.filtered.bcf.csi"
-		File ins_bcf = "${sample_name}.delly.ins.somatic.filtered.bcf"
-		File ins_bcf_index = "${sample_name}.delly.ins.somatic.filtered.bcf.csi"
-		File inv_bcf = "${sample_name}.delly.inv.somatic.filtered.bcf"
-		File inv_bcf_index = "${sample_name}.delly.inv.somatic.filtered.bcf.csi"
-		File bnd_bcf = "${sample_name}.delly.bnd.somatic.filtered.bcf"
-		File bnd_bcf_index = "${sample_name}.delly.bnd.somatic.filtered.bcf.csi"
+		File bcf = "${sample_name}.delly.del.somatic.filtered.bcf"
+		File bcf_index = "${sample_name}.delly.del.somatic.filtered.bcf.csi"
 	}
 }
 

workflow.wdl

@@ -70,16 +70,8 @@ workflow {{ project_name }} {
 
 	call bcf2vcf.bcf2vcf as bcf2vcf {
 		input:
-		ins_bcf=delly.ins_bcf,
-		ins_bcf_index=delly.ins_bcf_index,
-		del_bcf=delly.del_bcf,
-		del_bcf_index=delly.del_bcf_index,
-		dup_bcf=delly.dup_bcf,
-		dup_bcf_index=delly.dup_bcf_index,
-		inv_bcf=delly.inv_bcf,
-		inv_bcf_index=delly.inv_bcf_index,
-		bnd_bcf=delly.bnd_bcf,
-		bnd_bcf_index=delly.bnd_bcf_index,
+		bcf=delly.bcf,
+		bcf_index=delly.bcf_index,
 		docker=BCFdocker,
 		disk_size=disk_size,
 		cluster_config=SMALLcluster_config,