上传文件至 'tasks'

tasks/qualimap.wdl

@@ -0,0 +1,31 @@
+task qualimap{
+    String sample_id
+    File bam_file
+    File bam_bai
+    File annot_gff
+
+    String docker
+    String cluster_config
+    String disk_size
+
+    String out_dir = sample_id+'_BamQC'
+
+    command <<<
+        set -o pipefail
+        set -exo
+        nt=$(nproc)
+        /opt/qualimap/qualimap bamqc -bam ${bam_file} -gff ${annot_gff} -outformat PDF:HTML -nt $nt -outdir ${out_dir} --java-mem-size=32G
+        tar -zcvf ${out_dir}.tar ${out_dir}
+    >>>
+
+    runtime{
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output{
+        File out_file = "${out_dir}.tar"
+    }
+}