# HG changeset patch
# User davidvanzessen
# Date 1448462670 18000
# Node ID 7843e05bbb6c02d68ead9aa549148e4e7d46b2a1
# Parent  4b85fd44d94639fcb1550f5ed1742beac2f4f4bc
Uploaded

diff -r 4b85fd44d946 -r 7843e05bbb6c wrapper.sh
--- a/wrapper.sh	Wed Nov 25 05:38:22 2015 -0500
+++ b/wrapper.sh	Wed Nov 25 09:44:30 2015 -0500
@@ -10,7 +10,7 @@
 ext="${name##*.}"
 name="${name%.*}"
 name="${name// /_}"
-prefix="$name\"_\""
+prefix="${name}_"
 dir="$(cd "$(dirname "$0")" && pwd)"
 
 unzip $dir/fastqc_v0.11.2.zip -d $PWD/ > $PWD/unziplog.log
@@ -57,9 +57,9 @@
 			echo "<tr><td>$barcode</td><td>$count</td><td></td><td></td><td></td><td></td><td></td><td></td></tr>" >> $output
 			break
 		fi
-		file=$name"_"$barcode
-		mkdir $outDir/fastqc_$barcode
-		$workdir/FastQC/fastqc $file.fastq -o $outDir 2> /dev/null
+		file="${name}_${barcode}"
+		mkdir "$outDir/fastqc_$barcode"
+		$workdir/FastQC/fastqc "$file.fastq" -o "$outDir" 2> /dev/null
 		cat "$file.fastq" | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > "$file.fasta"
 		python $dir/trim.py --input "$file.fasta" --output "${file}_trimmed.fasta" --start "${trim_start[$barcode]}" --end "${trim_end[$barcode]}"
 		echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td><td><a href='${file}_trimmed.fasta'>${file}_trimmed.fasta</a></td><td><a href='${name}_${barcode}_fastqc.html'>Report</a></td></tr>" >> $output