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Trans_Struc_Gen.nf

+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+```c
+/*   
+ * Define the input parameters"""Takes input from csv-formatted file ("ID,Count") 
+                                     with counts for individual transcripts. 
+                                     Also a gtf-formatted file with exon coordinates 
+                                     of the transcripts included in the csv file. 
+                                     Outputs gtf-formatted file containing 
+                                     generated intron/exon structures per transcript.
+                                     Outputs csv-formatted file 
+                                     ("NewTranscriptID,ID,Count") with id of 
+                                     generated transcript, id of original 
+                                     transcript (without intron inclusions) and
+                                     Counts. 
+ */ 
+params.cvs_file = "$projectDir/tests/ #Input cvs file from group 1
+params.gtf_file = "$projectDir/tests/ #Input gtf file from group 1       
+params.outdir = "results" 
+
+
+/* Log some information for the user */
+
+log.info """\
+         R N A S E Q - N F   P I P E L I N E 
+         ===================================       
+         cvs_file     : ${params.cvs_file}      
+         gtf_file     : ${params.gtf_file}             
+         outdir       : ${params.outdir}          
+         """                                        
+         .stripIndent() 
+         
+/* 
+ * define the `file_validation` process
+ * given that the input files exist and are the correct format
+ */ 
+
+process file_validation { 
+
+    input:
+    path cvs_file
+    path gtf_file 
+    
+    output:
+    path cvs_file into struc_gen
+    path gtf_file into struc_gen
+    
+    script: 
+    """
+    
+    """ 
+}