Initial commit for PreprocessDragenVcf

wdl/PreprocessDragenVcf.wdl

@@ -0,0 +1,121 @@
+version 1.0
+
+workflow PreprocessDragenVcf {
+	input {
+		String sample_id            # Sample identifier
+		String vcf_path             # Path to the input VCF file
+		String sv_pipeline_docker   # Docker image path for GATK-SV
+		String svtk_docker          # Docker image path for svtk
+		File contigs_file          	# Path to the contigs file
+		Int min_size               	# Minimum size for standardization
+	}
+
+	call StandardizeVcf {
+		input:
+			sample_id = sample_id,
+			vcf_path = vcf_path,
+			contigs_file = contigs_file,
+			min_size = min_size,
+			svtk_docker = svtk_docker
+	}
+
+	call SortVcf {
+		input:
+			sample_id = sample_id,
+			vcf_path = StandardizeVcf.standardized_vcf,
+			sv_pipeline_docker = sv_pipeline_docker
+	}
+
+	call Vcf2Bed {
+		input:
+			sample_id = sample_id,
+			vcf_path = SortVcf.sorted_vcf,
+			sv_pipeline_docker = sv_pipeline_docker
+	}
+
+	output {
+		File vcf2bed_vapor = Vcf2Bed.vcf2bed_vapor
+	}
+}
+
+task StandardizeVcf {
+	input {
+		String sample_id            # Sample identifier
+		String vcf_path             # Path to the input VCF file
+		File contigs_file           # Path to the contigs file
+		Int min_size                # Minimum size for standardization
+		String svtk_docker          # Docker image path for svtk
+	}
+
+	command <<<
+		set -eu -o pipefail
+
+		svtk standardize \
+			--sample-names ~{sample_id} \
+			--contigs ~{contigs_file} \
+			--min-size ~{min_size} \
+			~{vcf_path} \
+			~{sample_id}.std_dragen.vcf.gz \
+			dragen
+	>>>
+
+	output {
+		File standardized_vcf = "~{sample_id}.std_dragen.vcf.gz"
+	}
+
+	runtime {
+		cpu: 1
+		memory: "2 GiB"
+		disks: "local-disk 2 HDD"
+		docker: svtk_docker
+	}
+}
+
+task SortVcf {
+	input {
+		String sample_id            # Sample identifier
+		File vcf_path               # Path to the standardized VCF file
+		String sv_pipeline_docker   # Docker image path for GATK-SV
+	}
+
+	command <<<
+		set -eu -o pipefail
+
+		bcftools sort -O z -o ~{sample_id}.std_dragen_sorted.vcf.gz ~{vcf_path}
+	>>>
+
+	output {
+		File sorted_vcf = "~{sample_id}.std_dragen_sorted.vcf.gz"
+	}
+
+	runtime {
+		cpu: 1
+		memory: "2 GiB"
+		disks: "local-disk 2 HDD"
+		docker: sv_pipeline_docker
+	}
+}
+
+task Vcf2Bed {
+	input {
+		String sample_id            # Sample identifier
+		File vcf_path             	# Path to the sorted VCF file
+		String sv_pipeline_docker   # Docker image path for GATK-SV
+	}
+
+	command <<<
+		set -eu -o pipefail
+		svtk vcf2bed --info SVTYPE --info SVLEN ~{vcf_path} - | awk '$7 != "BND"' > ~{sample_id}.bed
+	>>>
+
+	output {
+		File vcf2bed_vapor = "~{sample_id}.bed"
+	}
+
+	runtime {
+		cpu: 1
+		memory: "2 GiB"
+		disks: "local-disk 2 HDD"
+		docker: sv_pipeline_docker
+	}
+}