From 7ea70bf552bc22f5beef1fd7da6d3139803d7d30 Mon Sep 17 00:00:00 2001
From: Luca Cozzuto <lucacozzuto@gmail.com>
Date: Fri, 10 Aug 2018 13:35:12 +0200
Subject: [PATCH] some minor changes to the code

---
 lib/FeatureCounter.groovy |  2 +-
 lib/Misc.groovy           | 26 ++++++++++++++------------
 lib/PeakCaller.groovy     | 26 +++++++++++++-------------
 lib/QualityChecker.groovy |  8 ++++----
 4 files changed, 32 insertions(+), 30 deletions(-)

diff --git a/lib/FeatureCounter.groovy b/lib/FeatureCounter.groovy
index 5cb264b..a2f8213 100644
--- a/lib/FeatureCounter.groovy
+++ b/lib/FeatureCounter.groovy
@@ -26,7 +26,7 @@
     def public htseqCount() {
 
     """
-		htseq-count ${this.extrapars} -s ${this.strand} -f bam ${this.input} ${this.annotation} > ${this.output}
+		htseq-count ${this.extrapars} -s ${this.strand} -f bam ${this.input} ${this.annotation} ${this.extrapars} > ${this.output}
     """
 	}
 
diff --git a/lib/Misc.groovy b/lib/Misc.groovy
index 3a5b2e9..73c235b 100644
--- a/lib/Misc.groovy
+++ b/lib/Misc.groovy
@@ -100,11 +100,12 @@
     def public makeAlnProfilesWithDeepTools() {
 
 	"""
-		bamCoverage --bam ${this.input} -o ${this.output} \\
-    	--binSize 10 \\
-    	--normalizeUsing RPGC \\
-    	--effectiveGenomeSize ${this.genome_size} \\
-    	--extendReads  ${this.read_size}  \\
+		bamCoverage --bam ${this.input} -o ${this.output} \
+    	--binSize 10 \
+    	--normalizeUsing RPGC \
+    	--effectiveGenomeSize ${this.genome_size} \
+    	--extendReads  ${this.read_size}  \
+    	${this.extrapars} \
     	-p ${this.cpus} 
 	"""
 	}
@@ -136,13 +137,14 @@
     def public markDuplicateWithPicard() {
 
 		"""
-			java -jar ${this.java_path} MarkDuplicates \\
-        	INPUT=${this.input} \\
-        	OUTPUT=${this.output} \\
-        	ASSUME_SORTED=true \\
-        	REMOVE_DUPLICATES=true \\
-        	METRICS_FILE=${this.id}.metrics.txt \\
-        	VALIDATION_STRINGENCY=LENIENT 
+			java -jar ${this.java_path} MarkDuplicates \
+        	INPUT=${this.input} \
+        	OUTPUT=${this.output} \
+        	ASSUME_SORTED=true \
+        	REMOVE_DUPLICATES=true \
+        	METRICS_FILE=${this.id}.metrics.txt \
+        	VALIDATION_STRINGENCY=LENIENT \
+        	${this.extrapars}
 		"""
 	}
 	
diff --git a/lib/PeakCaller.groovy b/lib/PeakCaller.groovy
index 148055f..99c3640 100644
--- a/lib/PeakCaller.groovy
+++ b/lib/PeakCaller.groovy
@@ -45,12 +45,12 @@
 
     """
     export PYTHONPATH=""
-    macs2 callpeak \\
-        -t ${this.sample} \\
-        -f BAM \\
-        -n ${this.id} \\
-        --extsize ${this.frag_len} \\
-        ${extrapars} \\
+    macs2 callpeak \
+        -t ${this.sample} \
+        -f BAM \
+        -n ${this.id} \
+        --extsize ${this.frag_len} \
+        ${extrapars} \
 		-g ${this.genome_size} 2>${this.id}_log.txt
     """
 	}
@@ -61,13 +61,13 @@
     def private peakCallWithEpic() {
 
     """
-		epic --treatment ${this.sample} \\
-		     --control ${this.control} \\
-		     --chromsizes ${this.chr_sizes} \\
-		     --effective-genome-fraction ${this.genome_size} \\
-		     -o ${this.id}.out \\
-		     -b ${this.id}.bed \\
-		     --fragment-size ${this.frag_len} \\
+		epic --treatment ${this.sample} \
+		     --control ${this.control} \
+		     --chromsizes ${this.chr_sizes} \
+		     --effective-genome-fraction ${this.genome_size} \
+		     -o ${this.id}.out \
+		     -b ${this.id}.bed \
+		     --fragment-size ${this.frag_len} \
 		     ${extrapars}
     """
 	}
diff --git a/lib/QualityChecker.groovy b/lib/QualityChecker.groovy
index f7586ba..97fa9ef 100644
--- a/lib/QualityChecker.groovy
+++ b/lib/QualityChecker.groovy
@@ -116,7 +116,7 @@
 		-T "Fingerprints"  \
 		--plotFile ${this.output}.png \
 		--outRawCounts ${this.output}_rawcounts.tab \
-		--numberOfProcessors ${this.cpus} \
+		--numberOfProcessors ${this.cpus} ${this.extrapars} \
     """
 	}
 
@@ -133,7 +133,7 @@
 		 -b ${this.input} \
  		--smartLabels \
 		--outFileName ${this.output} \
-		--numberOfProcessors ${this.cpus} \
+		--numberOfProcessors ${this.cpus} ${this.extrapars} \
     """
 	}
 	
@@ -186,7 +186,7 @@
                               --regionBodyLength 5000 \
                               --afterRegionStartLength 3000 \
 							  --numberOfProcessors ${this.cpus} \
-                              --skipZeros -o ${this.output} 
+                              --skipZeros -o ${this.output} ${this.extrapars}
     """
 	}
 
@@ -205,7 +205,7 @@
 							  --beforeRegionStartLength 3000 \
 							  --afterRegionStartLength 3000 \
 							  --numberOfProcessors ${this.cpus} \
-							  --skipZeros -o ${this.output} 
+							  --skipZeros -o ${this.output} ${this.extrapars}
     """
 	}