Add WDL script for normalizing VCF files by removing HAPCOMP and HAPDOM fields"

wdl/malaria/NormalizeVCF.wdl

@@ -0,0 +1,122 @@
+version 1.0
+
+workflow NormalizeVCF {
+  input {
+    File input_vcf
+    File reference_fa
+    String sample_name  # New input for sample name
+    Int disk_size_gb = 50
+    Int memory_gb = 16
+    Int cpu_cores = 8
+  }
+
+  call RemoveHAPCOMP {
+    input:
+      input_vcf = input_vcf,
+      disk_size_gb = disk_size_gb,
+      memory_gb = memory_gb,
+      cpu_cores = cpu_cores
+  }
+
+  call RemoveHAPDOM {
+    input:
+      input_vcf = RemoveHAPCOMP.output_vcf,
+      disk_size_gb = disk_size_gb,
+      memory_gb = memory_gb,
+      cpu_cores = cpu_cores
+  }
+
+  call NormalizeVCFFile {
+    input:
+      input_vcf = RemoveHAPDOM.output_vcf,
+      reference_fa = reference_fa,
+      sample_name = sample_name,
+      disk_size_gb = disk_size_gb,
+      memory_gb = memory_gb,
+      cpu_cores = cpu_cores
+  }
+
+  output {
+    File normalized_vcf = NormalizeVCFFile.output_vcf
+    File normalized_vcf_index = NormalizeVCFFile.output_vcf_index
+  }
+}
+
+task RemoveHAPCOMP {
+  input {
+    File input_vcf
+    Int disk_size_gb
+    Int memory_gb
+    Int cpu_cores
+  }
+
+  command {
+    bcftools annotate -x 'INFO/HAPCOMP' ~{input_vcf} | bgzip -c > output.no_hapcomp.vcf.gz
+  }
+
+  output {
+    File output_vcf = "output.no_hapcomp.vcf.gz"
+  }
+
+  runtime {
+    docker: "us.gcr.io/broad-dsp-lrma/bcftools_htslib:v9152024"
+    memory: "~{memory_gb}G"
+    cpu: "~{cpu_cores}"
+    disks: "local-disk ~{disk_size_gb} SSD"
+  }
+}
+
+task RemoveHAPDOM {
+  input {
+    File input_vcf
+    Int disk_size_gb
+    Int memory_gb
+    Int cpu_cores
+  }
+
+  command {
+    bcftools annotate -x 'INFO/HAPDOM' ~{input_vcf} | bgzip -c > output.no_hapdom.vcf.gz
+  }
+
+  output {
+    File output_vcf = "output.no_hapdom.vcf.gz"
+  }
+
+  runtime {
+    docker: "us.gcr.io/broad-dsp-lrma/bcftools_htslib:v9152024"
+    memory: "~{memory_gb}G"
+    cpu: "~{cpu_cores}"
+    disks: "local-disk ~{disk_size_gb} SSD"
+  }
+}
+
+task NormalizeVCFFile {
+  input {
+    File input_vcf
+    File reference_fa
+    String sample_name  # Input for the sample name
+    Int disk_size_gb
+    Int memory_gb
+    Int cpu_cores
+  }
+
+  command {
+    # Normalize the VCF
+    bcftools norm -m -any --atom-overlaps . -f ~{reference_fa} ~{input_vcf} | bgzip -c > ~{sample_name}.norm.vcf.gz
+
+    # Index the normalized VCF with tabix (.tbi)
+    tabix -p vcf ~{sample_name}.norm.vcf.gz
+  }
+
+  output {
+    File output_vcf = "~{sample_name}.norm.vcf.gz"
+    File output_vcf_index = "~{sample_name}.norm.vcf.gz.tbi"
+  }
+
+  runtime {
+    docker: "us.gcr.io/broad-dsp-lrma/bcftools_htslib:v9152024"
+    memory: "~{memory_gb}G"
+    cpu: "~{cpu_cores}"
+    disks: "local-disk ~{disk_size_gb} SSD"
+  }
+}