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1 #!/bin/bash
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2
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3 source $(dirname $0)/util.sh
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4 source $1
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5
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6 INPUT_QUAL=$(extify qual ${INPUT_QUAL})
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7 BARCODES=$(extify csv ${BARCODES})
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8 RAW_SEQS=$(extify fasta ${RAW_SEQS})
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9
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10 seqmagick quality-filter \
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11 --input-qual ${INPUT_QUAL} \
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12 --barcode-file ${BARCODES} \
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13 --primer "${PRIMER}" \
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14 --report-out ${FILTER_REPORT} \
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15 --details-out ${FILTER_DETAILS} \
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16 --map-out ${SPLIT_MAP} \
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17 --barcode-header \
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18 --min-length ${MIN_LENGTH} \
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19 --min-mean-quality ${MIN_QUALITY} \
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20 --quality-window 30 \
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21 --quality-window-prop 0.9 \
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22 --quality-window-mean-qual 15 \
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23 ${RAW_SEQS} \
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24 filtered.fasta
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25
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26 if [[ ${REVERSE_COMPLEMENT} == "TRUE" ]]; then
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27 seqmagick mogrify \
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28 --reverse-complement \
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29 filtered.fasta
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30 fi
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31
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32 mv filtered.fasta ${FILTERED_SEQS}
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33
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34 # TODO: separate tool for concatenating seq data (and reverse complementing them?)
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35 #cat [12]*Reads.fasta | seqmagick convert --input-format fasta - combined.fasta --reverse-complement
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36 #cat [12]*.map.csv > combined.map.csv
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37
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38 sequencing_quality_report.py ${PLATE_JSON} -t "Sequencing quality report" -o ${SQR_DIR}
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39
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40 cat <<EOF > ${SQR}
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41 <!DOCTYPE HTML>
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42 <html lang="en-US">
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43 <head/>
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44 <body>
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45 <a href="index.html">Sequencing quality report</a>
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46 </body>
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47 </html>
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48 EOF
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