Mercurial > repos > davidvanzessen > sff_extract_demultiplex
comparison wrapper.sh @ 2:44ec2a1009fc draft
Uploaded
author | davidvanzessen |
---|---|
date | Wed, 21 Dec 2016 10:23:19 -0500 |
parents | cb08a27e5fc2 |
children |
comparison
equal
deleted
inserted
replaced
1:cbce7f35f8b0 | 2:44ec2a1009fc |
---|---|
62 $workdir/FastQC/fastqc "$file.fastq" -o "$outDir" 2> /dev/null | 62 $workdir/FastQC/fastqc "$file.fastq" -o "$outDir" 2> /dev/null |
63 cat "$file.fastq" | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > "$file.fasta" | 63 cat "$file.fastq" | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > "$file.fasta" |
64 python $dir/trim.py --input "$file.fasta" --output "${file}_trimmed.fasta" --start "${trim_start[$barcode]}" --end "${trim_end[$barcode]}" | 64 python $dir/trim.py --input "$file.fasta" --output "${file}_trimmed.fasta" --start "${trim_start[$barcode]}" --end "${trim_end[$barcode]}" |
65 echo "<tr><td>$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>" >> $output | 65 echo "<tr><td>$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 |
66 done < output.txt | 66 done < output.txt |
67 echo "</tbody></body></html>" >> $output | 67 |
68 echo "</tbody></table>" >> $output | |
69 cat $dir/results_footer.html >> $output | |
70 echo "</body></html>" >> $output |