上传文件至 'tasks'

tasks/ASCAT.wdl

@@ -0,0 +1,38 @@
+
+task ASCAT{
+    String sample
+    File tumor_bam
+    File tumor_bam_index
+    File? normal_bam
+    File? normal_bam_index
+    String gender
+    String ref_genome
+    String docker
+    String cluster_config
+    String disk_size
+
+    command <<<
+        set -o pipefail
+        set -e
+        
+        out_dir='./'
+         /root/miniconda3/envs/hrd/bin/Rscript /home/ASCAT/ascat.r tumor_bam normal_bam ${sample}+'_T' ${sample}+'_N' ${sample} WGS ${out_dir} ${gender} ${ref_genome}
+
+        ls ./
+
+        tar cvf ${sample}.tar ./
+
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output{
+        File out_file = "${sample}.tar"
+    }
+
+}