添加 'tasks/MSIsensor.wdl'

tasks/MSIsensor.wdl

@@ -0,0 +1,41 @@
+task MSIsensor {
+  
+  String sample
+  File ref_dir
+  String fasta
+  File tumor_bam
+  File tumor_bam_index
+  File? normal_bam
+  File? normal_bam_index
+  File baseline
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    # MSI
+    mkdir -p /cromwell_root/tmp/
+    msisensor-pro scan -d ${ref_dir}/${fasta} -o reference.list
+    if [ ${normal_bam} ]; then
+      msisensor-pro msi -d reference.list -n ${normal_bam} -t ${tumor_bam} -o /cromwell_root/tmp/${sample}
+    else
+      msisensor-pro pro -d ${baseline} -t ${tumor_bam} -o /cromwell_root/tmp/${sample}
+    fi
+    cp /cromwell_root/tmp/${sample} ${sample}.MSI.txt
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File msi = "${sample}.MSI.txt"
+  }
+}