Mercurial > repos > davidvanzessen > sff_extract_demultiplex
changeset 11:b59783f3d3ba draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 25 Nov 2015 05:35:25 -0500 |
| parents | 5a886d753c0a |
| children | 4b85fd44d946 |
| files | wrapper.sh |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- 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