调整匹配优先级

将匹配优先级调整为：miRNA > pre-miRNA > tRNA > RNA > piRNA

workflow.wdl

             docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
     }
 
-    call Align.AlignToSenseOnly as Align2piRNA {
+
+    call Align.AlignToSenseOnly as Align2tRNA {
         input:
             sample_id=sample_id,
             in_fastq=Align2PreMiRNA.out_fastq,
-            refname="piRNA",dir_index=dir_index_piRNA,prefix_index=prefix_index_piRNA,
+            refname="tRNA",dir_index=dir_index_tRNA,prefix_index=prefix_index_tRNA,
             max_mismatch_allowed=max_mismatch_allowed,
             docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
     }
 
-
-    call Align.AlignToSenseOnly as Align2tRNA {
+    call Align.AlignToSenseOnly as Align2RNA {
         input:
             sample_id=sample_id,
-            in_fastq=Align2piRNA.out_fastq,
-            refname="tRNA",dir_index=dir_index_tRNA,prefix_index=prefix_index_tRNA,
+            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.AlignToSenseOnly as Align2RNA {
+    call Align.AlignToSenseOnly as Align2piRNA {
         input:
             sample_id=sample_id,
-            in_fastq=Align2tRNA.out_fastq,
-            refname="RNA",dir_index=dir_index_RNA,prefix_index=prefix_index_RNA,
+            in_fastq=Align2RNA.out_fastq,
+            refname="piRNA",dir_index=dir_index_piRNA,prefix_index=prefix_index_piRNA,
             max_mismatch_allowed=max_mismatch_allowed,
             docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
     }
+
     call Align.AlignToBothStrand as Align2Hg38 {
         input:
             sample_id=sample_id,
-            in_fastq=Align2RNA.out_fastq,
+            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
             in_sam_align_RNA=Align2RNA.out_sam,
             cluster_config=cluster_config,disk_size=disk_size
     }
-}
+}