add preprocessing

wdl/pipelines/PacBio/Utility/MergePhasedVCF.wdl

@@ -12,13 +12,17 @@ workflow MergePhasedVCF{
         File reference_fasta_fai
     }
     call FindFiles{input: sampleFolder = SampleFolder}
+    scatter (bcf_file in FindFiles.vcfFiles){
+        call preprocess{input: bcf = bcf_file}
+    }
+
     call VU.CollectDefinitions as CD {
       input:
-      vcfs = FindFiles.vcfFiles
+      vcfs = preprocess.vcf
     }
     call VU.MergeAndSortVCFs as Merge {
       input:
-      vcfs = FindFiles.vcfFiles,
+      vcfs = preprocess.vcf,
       ref_fasta_fai = reference_fasta_fai,
       prefix = Samplename,
       header_definitions_file = CD.union_definitions
@@ -57,6 +61,33 @@ command {
     }
 }
 
+task preprocess {
+  input {
+    File bcf
+  }
+
+command {
+    bcftools view -Oz -o tmp.vcf.gz ~{bcf}
+    # bcftools sort -o whole_genome_sorted.vcf.gz tmp.vcf.gz
+    # bcftools index --tbi --force tmp.vcf.gz
+
+
+
+  }
+
+  output {
+    # Output the list of .bam files
+    File vcf = "tmp.vcf.gz"
+    # File whole_genome_vcf_tbi = "tmp.vcf.gz.tbi"
+
+  }
+
+    runtime {
+        docker: "us.gcr.io/broad-dsp-lrma/lr-basic:0.1.1"
+        disks: "local-disk 100 HDD"
+    }
+}
+
 task MergeVcf {
   input {
     Array[File] vcf_files

wdl/pipelines/TechAgnostic/Utility/ConvertToHailMTT2T.wdl

@@ -56,17 +56,17 @@ task preprocess {
 
 command {
     bcftools view -Oz -o tmp.vcf.gz ~{bcf}
-    bcftools sort -o whole_genome_sorted.vcf.gz tmp.vcf.gz
-    bcftools index --tbi --force whole_genome_sorted.vcf.gz
+    # bcftools sort -o whole_genome_sorted.vcf.gz tmp.vcf.gz
+    bcftools index --tbi --force tmp.vcf.gz
 
 
 
   }
 
   output {
     # Output the list of .bam files
-    File whole_genome_vcf = "whole_genome_sorted.vcf.gz"
-    File whole_genome_vcf_tbi = "whole_genome_sorted.vcf.gz.tbi"
+    File whole_genome_vcf = "tmp.vcf.gz"
+    File whole_genome_vcf_tbi = "tmp.vcf.gz.tbi"
 
   }