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

INSTALL.sh

@@ -7,12 +7,12 @@ bionext_ver="0.3"
 if [ -d "lib" ]; then {
 	echo "BioNextflow installed"
 } else {
-  		echo "BioNextflow not installed. Installing it..."
-		wget https://github.com/biocorecrg/BioNextflow/archive/${bionext_ver}.tar.gz
-		tar -zvxf ${bionext_ver}.tar.gz
-		mv "BioNextflow-${bionext_ver}/lib" .
-		rm ${bionext_ver}.tar.gz
-		rm -fr BioNextflow-${bionext_ver}
+  	echo "BioNextflow not installed. Installing it..."
+	wget https://github.com/biocorecrg/BioNextflow/archive/${bionext_ver}.tar.gz
+	tar -zvxf ${bionext_ver}.tar.gz
+	mv "BioNextflow-${bionext_ver}/lib" .
+	rm ${bionext_ver}.tar.gz
+	rm -fr BioNextflow-${bionext_ver}
 }
 fi
 

README.md

@@ -9,24 +9,24 @@ You need to install the library in your nextflow pipeline for being automaticall
 
 ### Code before
 
-        """
-     	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
-        """
+    """
+    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
-	def aligner = new NGSaligner(reference_file:genome_file, index:"genome_index", cpus:task.cpus)
-	aligner.doIndexing("bowtie")
+    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
 
-  sh INSTALL.sh 
+    sh INSTALL.sh 
 
 ### Get started