......

workflow.wdl

 import "./tasks/fastp.wdl" as fastp
 import "./tasks/hisat2.wdl" as hisat2
-import "./tasks/fastqc.wdl" as fastqc
-import "./tasks/multiqc.wdl" as multiqc
 import "./tasks/samtools.wdl" as samtools
-import "./tasks/fastqscreen.wdl" as fastqscreen
-import "./tasks/qualimapBAMqc.wdl" as qualimapBAMqc
 import "./tasks/stringtie.wdl" as stringtie
 
+import "./tasks/fastqc.wdl" as fastqc
+import "./tasks/fastqscreen.wdl" as fastqscreen
+import "./tasks/qualimapBAMqc.wdl" as qualimapBAMqc
+import "./tasks/multiqc.wdl" as multiqc
 
 workflow {{ project_name }} {
+	
 	File inputSamplesFile
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
+	
 	File screen_ref_dir
 	File fastq_screen_conf
-	File gtf
-	String fasta
-    	String sample_id
 	File read1
 	File read2
     	File idx
+
+	File gtf
+	String fasta
+    	String sample_id
+	
 	String adapter_sequence
     	String adapter_sequence_r2
 	String idx_prefix
 	scatter (quartet in inputSamples){
 
 		call fastp.fastp as fastp {
-			input: 
-            		sample_id=quartet[2],
-		    read1=quartet[0], 
-		    read2=quartet[1], 
-		    adapter_sequence=quartet[3], 
-		    adapter_sequence_r2=quartet[4]
+		input: 
+		sample_id=quartet[2],
+		read1=quartet[0], 
+		read2=quartet[1], 
+		adapter_sequence=quartet[3], 
+		adapter_sequence_r2=quartet[4]
 		}
 
 		call fastqc.fastqc as fastqc {
-		    input:
-		    read1=fastp.Trim_R1, 
-		    read2=fastp.Trim_R2
+		input:
+		read1=fastp.Trim_R1, 
+		read2=fastp.Trim_R2
 		}
 
 		call fastqscreen.fastqscreen as fastqscreen {
-            input:
-            read1=fastp.Trim_R1, 
-		    read2=fastp.Trim_R2,
-			screen_ref_dir=screen_ref_dir,
-			fastq_screen_conf=fastq_screen_conf
+		input:
+		read1=fastp.Trim_R1, 
+		read2=fastp.Trim_R2,
+		screen_ref_dir=screen_ref_dir,
+		fastq_screen_conf=fastq_screen_conf
 		}
 
 		call hisat2.hisat2 as hisat2 {
-			input: 
-		    sample_id=quartet[2],
-		    idx=idx, 
-		    idx_prefix=idx_prefix, 
-		    Trim_R1=fastp.Trim_R1, 
-		    Trim_R2=fastp.Trim_R2
+		input: 
+		sample_id=quartet[2],
+		idx=idx, 
+		idx_prefix=idx_prefix, 
+		Trim_R1=fastp.Trim_R1, 
+		Trim_R2=fastp.Trim_R2
 		}
 
-        call samtools.samtools as samtools {
-            input: 
-		    sample_id=quartet[2],
-		    sam = hisat2.sam 
-            }
+		call samtools.samtools as samtools {
+		input: 
+		sample_id=quartet[2],
+		sam = hisat2.sam 
+            	}
         
-        call qualimapBAMqc.qualimapBAMqc as qualimapBAMqc {
-			input:
-			bam= samtools.out_bam
+        	call qualimapBAMqc.qualimapBAMqc as qualimapBAMqc {
+		input:
+		bam= samtools.out_bam
 		}
 
 
-        call stringtie.stringtie as stringtie {
-              input: 
-		    sample_id=quartet[2],
-            		gtf = gtf, 
-		    bam = samtools.out_bam
+		call stringtie.stringtie as stringtie {
+		input: 
+		sample_id=quartet[2],
+		gtf = gtf, 
+		bam = samtools.out_bam
+		}
 	}
-}
 
 
 	call multiqc.multiqc as multiqc {
-		input:
-		read1_zip=fastqc.read1_zip,
-		read2_zip=fastqc.read2_zip,
-		txt1=fastqscreen.txt1,
-		txt2=fastqscreen.txt2,
-		rnaseq_zip=qualimapRNAseq.rnaseq_zip
+	input:
+	read1_zip=fastqc.read1_zip,
+	read2_zip=fastqc.read2_zip,
+	txt1=fastqscreen.txt1,
+	txt2=fastqscreen.txt2,
+	rnaseq_zip=qualimapRNAseq.rnaseq_zip
 	}
 }