更新 'workflow.wdl'

workflow.wdl

 
     File dir_index_miRNA
     String prefix_index_miRNA
+    File dir_index_RNA
+    String prefix_index_RNA
     File dir_index_rn7
     String prefix_index_rn7
 
             docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
     }
 
-    call Align.AlignToBothStrand as Align2rn7 {
+    call Align.AlignToSenseOnly as Align2RNA {
         input:
             sample_id=sample_id,
-            in_fastq=ReadFilter.out_fastq,
-            refname="rn7",dir_index=dir_index_rn7,prefix_index=prefix_index_rn7,
+            in_fastq=Align2tRNA.out_fastq,
+            refname="RNA",dir_index=dir_index_RNA,prefix_index=prefix_index_RNA,
+            max_mismatch_allowed=max_mismatch_allowed,
+            docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
+    }
+
+    call Align.AlignToBothStrand as Align2RN7 {
+        input:
+            sample_id=sample_id,
+            in_fastq=Align2piRNA.out_fastq,
+            refname="Hg38",dir_index=dir_index_hg38,prefix_index=prefix_index_hg38,
             max_mismatch_allowed=max_mismatch_allowed,
             docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
     }
         input:
             sample_id=sample_id,
             in_log_trimAdatper=TrimAdapt.out_log,in_log_readFilter=ReadFilter.out_log,
-            in_log_align_miRNA=Align2miRNA.out_log,in_log_align_rn7=Align2rn7.out_log,
+            in_log_align_miRNA=Align2miRNA.out_log,in_log_align_RNA=Align2RNA.out_log,in_log_align_rn7=Align2RN7.out_log,
+            in_sam_align_RNA=Align2RNA.out_sam,
             cluster_config=cluster_config,disk_size=disk_size
     }
-}
+}