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workflow.wdl

         File idx
 	String idx_prefix
         File gtf
+	String sample_id
 	
 	
 	call hisat2.hisat2 as hisat2 {
-		input: idx=idx, idx_prefix=idx_prefix, read1=read1, read2=read2
+		input: 
+	idx=idx, 
+	idx_prefix=idx_prefix, 
+	read1=read1,
+	read2=read2,
+	sample_id=sample_id
 	}
 
         call samtools.samtools as samtools {
-               input: sam = hisat2.sam
+               input: 
+	sample_id=sample_id, 
+	sam = hisat2.sam
 	}
 
         call stringtie.stringtie as stringtie {
-              input: gtf = gtf, bam = samtools.out_bam
+              input: 
+	gtf = gtf, 
+	bam = samtools.out_bam,
+	sample_id=sample_id
 	}