添加 'tasks/bcftools.wdl'

tasks/bcftools.wdl

@@ -0,0 +1,31 @@
+task bcftools {
+  
+  File ref_dir
+  String fasta
+  File vcf
+  String basename = basename(vcf,".vcf")
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    # bcftools norm -m -both ${vcf} | bcftools norm -f ${ref_dir}/${fasta} -Ov -o ${basename}.norm.vcf
+    # Split multiallelic sites
+    bcftools norm -m -both ${vcf} -o ${basename}.norm.vcf
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File norm_vcf = "${basename}.norm.vcf"
+  }
+}