Mercurial > repos > davidvanzessen > sff_extract_demultiplex
changeset 13:7843e05bbb6c draft default tip
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 25 Nov 2015 09:44:30 -0500 |
| parents | 4b85fd44d946 |
| children | |
| files | wrapper.sh |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- 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