添加 'tasks/Haplotyper.wdl'

tasks/Haplotyper.wdl

@@ -0,0 +1,49 @@
+task Haplotyper {
+  
+  File ref_dir
+  String fasta
+  File dbsnp_dir
+  
+  String SENTIEON_LICENSE
+  File recaled_bam
+  File recaled_bam_index
+  String dbsnp
+  String sample
+  String docker
+  String cluster_config
+  String disk_size
+  
+  File? regions
+  Int? interval_padding
+  
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+    else
+      INTERVAL=""
+    fi
+
+    sentieon driver -t $nt \
+    --interval ${regions} -r ${ref_dir}/${fasta} \
+    -i ${recaled_bam} \
+    --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} \
+    ${sample}.Haplotyper.vcf
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File vcf = "${sample}.Haplotyper.vcf"
+    File vcf_idx = "${sample}.Haplotyper.vcf.idx"
+  }
+}