同步至HPC-v20190527版

增加Unaligned片段成分分析

workflow.wdl

@@ -1,3 +1,4 @@
+import "./tasks/Fastqc.wdl" as Fastqc
 import "./tasks/TrimAdapt.wdl" as TrimAdapt
 import "./tasks/ReadFilter.wdl" as ReadFilter
 import "./tasks/Align.wdl" as Align
@@ -5,38 +6,58 @@ import "./tasks/Quantification.wdl" as Quantification
 import "./tasks/ReadStats.wdl" as ReadStats
 
 workflow {{ project_name }} {
-
-    String sample_ID
+    String sample_id
     File raw_fastq
-    
-    String docker_fastp
-    String docker_bowtie
-
-    String cluster_config
-    String disk_size
 
     String adapter_seq
     Int randomBase_in_adapter
-    
+    Int sequencing_length
+
     Int qualified_quality_phred
     Int unqualified_percent_limit
     Int n_base_limit
     Int length_required
 
-    File dir_index_mature
-    String prefix_index_mature
-    Int sum_unmatch_quality_limit
+    Int max_mismatch_allowed
+
+    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
+
+    String docker_fastqc
+    String docker_fastp
+    String docker_bowtie
+
+    String cluster_config
+
+    String disk_size
+
+    call Fastqc.Fastqc as Fastqc {
+        input:
+            in_fastq=raw_fastq,
+            docker=docker_fastqc, cluster_config=cluster_config, disk_size=disk_size
+    }
 
     call TrimAdapt.TrimAdapt as TrimAdapt {
         input:
-            sample_ID=sample_ID,in_fastq=raw_fastq,
-            adapter_seq=adapter_seq, randomBase_in_adapter=randomBase_in_adapter,
+            sample_id=sample_id,in_fastq=raw_fastq,
+            adapter_seq=adapter_seq, randomBase_in_adapter=randomBase_in_adapter, sequencing_length=sequencing_length,
             docker=docker_fastp, cluster_config=cluster_config, disk_size=disk_size
     }
 
+
     call ReadFilter.ReadFilter as ReadFilter {
         input:
-            sample_ID=sample_ID,
+            sample_id=sample_id,
             in_fastq=TrimAdapt.out_fastq,
             qualified_quality_phred=qualified_quality_phred,unqualified_percent_limit=unqualified_percent_limit,
             n_base_limit=n_base_limit,
@@ -44,29 +65,73 @@ workflow {{ project_name }} {
             docker=docker_fastp, cluster_config=cluster_config, disk_size=disk_size
     }
 
-    call Align.Align as Align2Mature {
+    call Align.AlignToSenseOnly as Align2miRNA {
         input:
-            sample_ID=sample_ID,
+            sample_id=sample_id,
             in_fastq=ReadFilter.out_fastq,
-            dir_index=dir_index_mature,prefix_index=prefix_index_mature,
-            sum_unmatch_quality_limit=sum_unmatch_quality_limit,
+            refname="miRNA",dir_index=dir_index_miRNA,prefix_index=prefix_index_miRNA,
+            max_mismatch_allowed=max_mismatch_allowed,
+            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 Quantification.Quantification as Quantification{
+    call Align.AlignToSenseOnly as Align2piRNA {
         input:
-            sample_ID=sample_ID,
-            in_sam=Align2Mature.out_sam,
-            cluster_config=cluster_config, disk_size=disk_size
+            sample_id=sample_id,
+            in_fastq=Align2PreMiRNA.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 ReadStats.ReadStats as ReadStats {
+
+    call Align.AlignToSenseOnly as Align2tRNA {
+        input:
+            sample_id=sample_id,
+            in_fastq=Align2piRNA.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_log_trimAdatper=TrimAdapt.out_log,
-            in_log_readFilter=ReadFilter.out_log,
-            in_log_align_mature=Align2Mature.out_log,
-            cluster_config=cluster_config, disk_size=disk_size
+            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.AlignToBothStrand as Align2Hg38 {
+        input:
+            sample_id=sample_id,
+            in_fastq=Align2RNA.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
+    }
+
+    call Quantification.Quantification as Quantification {
+        input:
+            sample_id=sample_id,
+            in_sam=Align2miRNA.out_sam,
+            cluster_config=cluster_config,disk_size=disk_size
     }
 
-}
+    call ReadStats.ReadStats as ReadStats {
+        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,
+            cluster_config=cluster_config,disk_size=disk_size
+    }
+}