Adding Reporter, changing QC to QualityChecker

lib/QC.groovy → lib/QualityChecker.groovy

@@ -5,7 +5,7 @@
  * Luca Cozzuto <lucacozzuto@gmail.com>
  */
 
- class QC {
+ class QualityChecker {
 
 	/*
 	 * Properties definition

lib/Reporter.groovy

@@ -0,0 +1,104 @@
+/* 
+ * Class for making reports, file descriptors, etc  
+ *
+ * @authors
+ * Luca Cozzuto <lucacozzuto@gmail.com>
+ */
+
+ class Reporter {
+
+	/*
+	 * Properties definition
+	 */
+
+     String email = ''
+     String id = ''
+     String title = ''
+     String subtitle = ''
+     String strand = ''
+     String extension = ''
+     String type = ''
+     String file_name = ''
+     String PI = ''
+     String user = ''
+     String config_file = ''
+
+
+    def public test() {
+        output = this.dump()
+    """
+     echo '${output}'
+    """
+    }
+
+   /* 
+    * Method for writing files needed for an HUB @ UCSC Genome Browser
+    */
+
+    def public makeGenomeUcscHub() {
+
+    """
+		echo "genome ${this.id}
+trackDb ${this.id}/trackDb.txt" > genomes.txt;
+		echo "hub ${this.id}
+shortLabel ${this.title}
+longLabel ${this.subtitle}
+genomesFile genomes.txt
+email ${this.email}" > hub.txt 
+    """
+    }
+
+   /* 
+    * Method for writing track DB file needed for HUB @ UCSC Genome Browser
+    */
+    def public makeBigWigTrackDB() {
+
+	    """
+	    echo "track ${this.id} 
+type ${this.type}  
+compositeTrack on 
+shortLabel RNAseq profiles (${this.title})
+longLabel RNAseq profiles (${this.subtitle})
+visibility full
+color 0,0,255
+autoScale on
+maxHeightPixels 128:60:11
+" >>  trackDb.txt;
+	for i in *.${this.extension}; \\
+	do NAME=`echo \$i | sed s/\\.${this.extension}//g`; \\
+	echo track \$NAME; \\
+	echo bigDataUrl \$i; \\
+	echo shortLabel \$NAME; \\
+	echo longLabel \$NAME; \\
+	echo "type ${this.type}"; \\
+	echo "parent ${this.id}"; \\
+	echo ""; \\
+	done >> trackDb.txt;
+	"""
+	}
+
+   /* 
+    * Method for writing multiQC report in a super custom way
+    */
+    def public makeMultiQCreport() {
+
+	"""
+echo "title: \"${this.title}\"
+subtitle: \"${this.subtitle}\"
+intro_text: False
+
+report_header_info:
+    - PI: ${this.PI}
+    - User: ${this.user}
+    - Date: `date`
+    - Contact E-mail: \'${this.email}\'  
+    - Application Type: \'ChIP-seq\'
+    - Reference Genome: \'${this.id}\'
+" > config.yaml;
+cat ${this.config_file} >> config.yaml;   
+	    multiqc -c config.yaml .
+	"""
+	}
+
+
+}

testFunctions.nf

@@ -27,16 +27,12 @@
  */
 
 
-/* 
- * Check that helper function `mappingPairsWithSTAR` returns the exepcted result
-
- */
 
 	process testFunction {
 	echo true
 
 		script:
-	myclass = new NGSaligner2(reads:"luca.fastq", output:"toni.qual")
+	def myclass = new QC(input:"luca.fastq", output:"toni.qual")
 	myclass.test()
 	}