更新 'workflow.wdl'

workflow.wdl

@@ -1,33 +1,23 @@
-import "./tasks/samtools_index.wdl" as samtools_index
 import "./tasks/spladder.wdl" as spladder
 
 
 workflow {{ project_name }} {
     String sample_id
-    File bam_file
+    File bam
+    File bai
     File reference_gtf_file
     
 
     String spladder_docker
     String spladder_cluster
-    String samtools_docker
-    String samtools_cluster
     String disk_size	
 
-	call samtools_index.samtools_index as samtools_index {
-		input:
-		bam_file=bam_file,
-		docker=samtools_docker,
-		cluster_config=samtools_cluster,
-		disk_size=disk_size
-	}
-
 	call spladder.spladder as spladder {
 		input:
 		reference_gtf_file=reference_gtf_file,
 		sample_id=sample_id,
-		bam=samtools_index.bam,
-		bai=samtools_index.bai,
+		bam=bam,
+		bai=bai,
 		docker=spladder_docker,
 		cluster=spladder_cluster,
 		disk_size=disk_size