adding support to salmon and skewer

biocorecrg · May 16, 2018 · 596bb3f · 596bb3f
1 parent 5f8aa45
commit 596bb3f
Showing 1 changed file with 21 additions and 0 deletions.
diff --git a/lib/Trimming.groovy b/lib/Trimming.groovy
@@ -0,0 +1,21 @@
+/* 
+ * Repository for biological functions
+ *
+ * @authors
+ * Luca Cozzuto <lucacozzuto@gmail.com>
+ */
+
+ class Trimming {
+
+	/* 
+	 * Function for trimming read pairs with Skewer
+ 	 */
+
+    static def trimPairsWithSkewer( pair_id, reads, minread, cpus, extrapars="", debug="no") { 
+	    """
+		if [ `echo ${debug} == "debug"` ]; then print="echo "; else print=""; fi
+		\$print	skewer ${extrapars} -t ${cpus} -l ${minread} -n -u -o ${pair_id} -z ${reads}
+        """
+     }
+
+}