上传文件至 'tasks'

tasks/samtools.wdl

@@ -0,0 +1,29 @@
+task samtools {
+    File bam_file
+    String bam_id = basename(bam_file)
+
+    String docker
+    String cluster
+    String disk_size
+
+
+    command <<<
+       set -o pipefail
+       set -e
+
+       samtools index ${bam_file}
+
+    >>>
+
+    runtime {
+       docker: docker
+       cluster: cluster
+       systemDisk: "cloud_ssd 40"
+       dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+      File bam_index = "$(bam_id).bai"
+    }
+
+}