adding support to salmon and skewer

lib/Misc.groovy

@@ -10,8 +10,7 @@
 
 	/* 
 	 * Function for running fastQC on input samples
- 	 */
-
+ 	 */	
     static def samtoolSort(bamfile, sortedfile, cpus="1", debug="no") {
 
     """
@@ -21,6 +20,24 @@
 		fi
     """
 	}
+
+	/* 
+	 * Function for running fastQC on input samples
+ 	 */
+    static def getTranscriptsFromGTF(genome_file, annotation, output="transcript.fa", debug="no") {
+
+    """
+    	if [ `echo ${debug} == "debug"` ]; then print="echo "; else print=""; fi	
+     	if [ `echo ${genome_file} | grep ".gz"` ]; then 
+			\$print zcat ${genome_file} > `basename ${genome_file} .gz`
+			\$print gffread -g `basename ${genome_file} .gz` -w ${output} ${annotation}
+        	\$print rm `basename ${genome_file} .gz`
+        else \$print gffread -g ${genome_file} -w ${output} ${annotation}
+		fi
+    """
+	}
+
+
 
 
 

lib/NGSaligner.groovy

@@ -24,6 +24,38 @@
 		fi
         """
     }
+
+    /*
+	 * Indexing a transcriptome with Salmon mapper. It reads both gzipped and plain fasta
+ 	 */
+
+    static def indexWithSalmon( transcript_file, indexname="transcript.index", kmer, cpus, extrapars="", debug="no") { 
+
+        """	
+		if [ `echo ${transcript_file} | grep ".gz"` ]; then 
+			zcat ${transcript_file} > `basename ${transcript_file} .gz`;
+   		    salmon index -t `basename ${transcript_file} .gz` -i ${indexname} --type quasi -k ${kmer} ${extrapars} -p ${cpus};
+   		    rm `basename ${transcript_file} .gz`;
+		else salmon index -t ${transcript_file} -i ${indexname} --type quasi -k ${kmer} ${extrapars} -p ${cpus}
+		fi
+        """
+    }
+
+    /*
+	 * Mapping to a transcriptome index with Salmon mapper. 
+ 	 */
+
+    static def mapPEWithSalmon( transcript_index, readsA, readsB, output, libtype="ISF", cpus, extrapars="", debug="no") { 
+
+        """	
+                
+		if [ `echo ${readsA} | grep ".gz"` ]; then 
+			        salmon quant -i ${transcript_index} --gcBias -l ${libtype} -1 <(gunzip -c ${readsA}) -2 <(gunzip -c ${readsB}) ${extrapars} -o ${output}
+		else         salmon quant -i ${transcript_index} --gcBias -l ${libtype} -1 ${readsA} -2 ${readsB} ${extrapars} -o ${output}
+		fi
+        """
+    }
+
 
 	/*
 	 * Mapping SE and PE reads with Bowtie2. Reads can be both gzipped and plain fastq