更新 'workflow.wdl'

workflow.wdl

@@ -22,14 +22,6 @@ workflow {{ project_name }} {
 
     File dir_index_miRNA
     String prefix_index_miRNA
-    File dir_index_preMiRNA
-    String prefix_index_preMiRNA
-    File dir_index_piRNA
-    String prefix_index_piRNA
-    File dir_index_tRNA
-    String prefix_index_tRNA
-    File dir_index_RNA
-    String prefix_index_RNA
     File dir_index_hg38
     String prefix_index_hg38
 
@@ -74,43 +66,6 @@ workflow {{ project_name }} {
             docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
     }
 
-    call Align.AlignToSenseOnly as Align2PreMiRNA {
-        input:
-            sample_id=sample_id,
-            in_fastq=Align2miRNA.out_fastq,
-            refname="preMiRNA",dir_index=dir_index_preMiRNA,prefix_index=prefix_index_preMiRNA,
-            max_mismatch_allowed=max_mismatch_allowed,
-            docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
-    }
-
-
-    call Align.AlignToSenseOnly as Align2tRNA {
-        input:
-            sample_id=sample_id,
-            in_fastq=Align2PreMiRNA.out_fastq,
-            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 Align2RNA {
-        input:
-            sample_id=sample_id,
-            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 Align2piRNA {
-        input:
-            sample_id=sample_id,
-            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,
@@ -131,8 +86,7 @@ workflow {{ project_name }} {
         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_preMiRNA=Align2PreMiRNA.out_log,in_log_align_piRNA=Align2piRNA.out_log,in_log_align_tRNA=Align2tRNA.out_log,in_log_align_RNA=Align2RNA.out_log,in_log_align_hg38=Align2Hg38.out_log,
-            in_sam_align_RNA=Align2RNA.out_sam,
+            in_log_align_miRNA=Align2miRNA.out_log,in_log_align_hg38=Align2Hg38.out_log,
             cluster_config=cluster_config,disk_size=disk_size
     }
 }