更新 'tasks/samtools_index.wdl'

tasks/samtools.wdl

@@ -1,27 +0,0 @@
-task samtools {
-    File bam_file
-    String bam_id=basename(bam_file)
-    String docker
-    String cluster
-    String disk_size
-
-
-    command <<<
-       samtools index --help
-       samtools index -b ${bam_file} > ./${bam_id}.bai
-       cp ${bam_file} ./                               
-    >>>
-
-    runtime {
-       docker: docker
-       cluster: cluster
-       systemDisk: "cloud_ssd 40"
-       dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-
-    output {
-      File bam="${bam_id}"      
-      File bam_index="${bam_id}.bai"
-    }
-
-}

tasks/samtools_index.wdl

@@ -0,0 +1,25 @@
+task samtools_index {
+	File bam_file
+	String docker
+	String cluster_config
+	String disk_size
+	
+	String clean_bam_name = basename(bam_file)
+	
+	command <<<
+	    samtools index --help
+		samtools index ${bam_file} ${clean_bam_name}.bai
+		cp ${bam_file} ./${clean_bam_name}                      
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File bai = "${clean_bam_name}.bai"
+		File bam = "${clean_bam_name}"          
+	}
+}