上传文件至 'tasks'

tasks/count.wdl

@@ -0,0 +1,26 @@
+task count {
+    File gene_abundance
+    Array[File] ballgown
+    String sample_id
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+      mkdir -p /cromwell_root/tmp/${sample_id}
+      cp -r ${sep=" " ballgown} /cromwell_root/tmp/${sample_id}
+      count -g ${sample_id}_gene_count_matrix.csv -t ${sample_id}_transcript_count_matrix.csv
+    >>>
+    
+    runtime {
+      docker: docker
+      cluster: cluster
+      systemDisk: "cloud_ssd 40"
+      dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+    
+    output {
+      File mat_expression_genecount = "${sample_id}_gene_count_matrix.csv"
+      File mat_expression_transcriptcount = "${sample_id}_transcript_count_matrix.csv"
+    }
+}