Merge pull request #352 from RoanKanninga/master

fixed Illumina2Gaf2FastQ for None barcodes
molgenis · Nov 11, 2015 · 9ca4c13 · 9ca4c13
2 parents 895c503 + b83aca2
commit 9ca4c13
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/compute5/NGS_Demultiplex/protocols/Illumina2GafFastQ.sh b/compute5/NGS_Demultiplex/protocols/Illumina2GafFastQ.sh
@@ -25,13 +25,13 @@ do
                         # Process lane FastQ files for lane without barcodes or with GAF barcodes.
 			cd ${intermediateDir}
 
-			md5sum lane${lane}_S[0-9]*_L00${lane}_R1_001.fastq.gz >  ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}.fq.gz.md5
+			md5sum lane${lane}_None_S[0-9]*_L00${lane}_R1_001.fastq.gz >  ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}.fq.gz.md5
 
-			cp lane${lane}_S[0-9]*_L00${lane}_R1_001.fastq.gz ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}.fq.gz
+			cp lane${lane}_None_S[0-9]*_L00${lane}_R1_001.fastq.gz ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}.fq.gz
 
 			cd  ${runResultsDir}
 			VAR1=${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}.fq.gz
-			perl -pi -e "s|lane${lane}_S[0-9]+_L00${lane}_R1_001.fastq.gz|$VAR1|" $VAR1.md5
+			perl -pi -e "s|lane${lane}_None_S[0-9]+_L00${lane}_R1_001.fastq.gz|$VAR1|" $VAR1.md5
 
 			md5sum -c ${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}.fq.gz
 		###CORRECT BARCODES
@@ -61,19 +61,19 @@ else
 		if [[ ${barcode[sampleNumber]} == "None" ]]
     		then
 		cd ${intermediateDir}
-		md5sum lane${lane}_S[0-9]*_L00${lane}_R1_001.fastq.gz >  ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_1.fq.gz.md5
-		md5sum lane${lane}_S[0-9]*_L00${lane}_R2_001.fastq.gz >  ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_2.fq.gz.md5
+		md5sum lane${lane}_None_S[0-9]*_L00${lane}_R1_001.fastq.gz >  ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_1.fq.gz.md5
+		md5sum lane${lane}_None_S[0-9]*_L00${lane}_R2_001.fastq.gz >  ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_2.fq.gz.md5
 
-		cp lane${lane}_S[0-9]*_L00${lane}_R1_001.fastq.gz ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_1.fq.gz
-		cp lane${lane}_S[0-9]*_L00${lane}_R2_001.fastq.gz ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_2.fq.gz
+		cp lane${lane}_None_S[0-9]*_L00${lane}_R1_001.fastq.gz ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_1.fq.gz
+		cp lane${lane}_None_S[0-9]*_L00${lane}_R2_001.fastq.gz ${runResultsDir}/${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_2.fq.gz
 
 		cd  ${runResultsDir}
 
 		VAR1=${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_1.fq.gz
 		VAR2=${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_2.fq.gz
 
-		perl -pi -e "s|lane${lane}_S[0-9]+_L00${lane}_R1_001.fastq.gz|$VAR1|" $VAR1.md5
-                perl -pi -e "s|lane${lane}_S[0-9]+_L00${lane}_R2_001.fastq.gz|$VAR2|" $VAR2.md5
+		perl -pi -e "s|lane${lane}_None_S[0-9]+_L00${lane}_R1_001.fastq.gz|$VAR1|" $VAR1.md5
+                perl -pi -e "s|lane${lane}_None_S[0-9]+_L00${lane}_R2_001.fastq.gz|$VAR2|" $VAR2.md5
 
 		md5sum -c ${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_1.fq.gz.md5
 		md5sum -c ${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}_2.fq.gz.md5