# HG changeset patch
# User davidvanzessen
# Date 1448447725 18000
# Node ID b59783f3d3baf02328cfc0c8189d69b9df929b68
# Parent  5a886d753c0a3171d59483585e3b38647e0e22fb
Uploaded

diff -r 5a886d753c0a -r b59783f3d3ba wrapper.sh
--- a/wrapper.sh	Wed Nov 25 05:02:54 2015 -0500
+++ b/wrapper.sh	Wed Nov 25 05:35:25 2015 -0500
@@ -9,7 +9,7 @@
 name=$(basename "$7")
 ext="${name##*.}"
 name="${name%.*}"
-prefix=$name"_"
+prefix="$name\"_\""
 dir="$(cd "$(dirname "$0")" && pwd)"
 
 unzip $dir/fastqc_v0.11.2.zip -d $PWD/ > $PWD/unziplog.log
@@ -59,8 +59,8 @@
 		file=$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]}
+		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
 done < output.txt
 echo "</tbody></body></html>" >> $output