Initial version

workflow.wdl

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+import "./tasks/TrimAdapt.wdl" as TrimAdapt
+import "./tasks/ReadFilter.wdl" as ReadFilter
+import "./tasks/Align.wdl" as Align
+import "./tasks/Quantification.wdl" as Quantification
+import "./tasks/ReadStats.wdl" as ReadStats
+
+workflow {{ project_name }} {
+
+    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 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
+
+    call TrimAdapt.TrimAdapt as TrimAdapt {
+        input:
+            sample_ID=sample_ID,in_fastq=raw_fastq,
+            adapter_seq=adapter_seq, randomBase_in_adapter=randomBase_in_adapter,
+            docker=docker_fastp, cluster_config=cluster_config, disk_size=disk_size
+    }
+
+    call ReadFilter.ReadFilter as ReadFilter {
+        input:
+            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,
+            length_required=length_required,
+            docker=docker_fastp, cluster_config=cluster_config, disk_size=disk_size
+    }
+
+    call Align.Align as Align2Mature {
+        input:
+            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,
+            docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
+    }
+
+    call Quantification.Quantification as Quantification{
+        input:
+            sample_ID=sample_ID,
+            in_sam=Align2Mature.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_mature=Align2Mature.out_log,
+            cluster_config=cluster_config, disk_size=disk_size
+    }
+
+}