Merge branch 'master' of github.com:biocorecrg/BioNextflow

README.md

@@ -10,17 +10,18 @@ You need to install the library in your nextflow pipeline for being automaticall
 ### Code before
 
         """
-        if [ `echo ${genome_file} | grep ".gz"` ]; then 
-                zcat ${genome_file} > `basename ${genome_file} .gz`
-                bowtie2-build --threads ${cpus} `basename ${genome_file} .gz` ${indexname}
-                rm `basename ${genome_file} .gz`
-                else bowtie2-build --threads ${cpus} ${genome_file} ${indexname}
-                fi
+     	if [ `echo ${reference_file} | grep ".gz"` ]; then 
+		zcat ${reference_file} > ${index}.fa			
+        	bowtie-build --threads ${task.cpus} ${index}.fa ${index}
+	else 
+                ln -s ${reference_file} ${index}.fa 
+	        bowtie-build --threads ${tasks.cpus} ${index}.fa ${index}
+	fi
         """
 
 ### Code after
-    aligner = new(genome_file:genome_file, index:bowtie2genome", cpus:task.cpus)
-    aligner.doAlignment()
+	def aligner = new NGSaligner(reference_file:genome_file, index:"genome_index", cpus:task.cpus)
+	aligner.doIndexing("bowtie")
 
 ### Installation
 Edit the INSTALL.sh file to select the required version