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https://github.com/MillironX/sc2-sequencing.git
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24 lines
742 B
Bash
24 lines
742 B
Bash
#!/bin/bash
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# Combines the output from the ONT GridION into a single compressed fastq file
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# Initiation, get some important info
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RUNNAME=$(basename "${1}")
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NUMCPU=$(grep -c processor < /proc/cpuinfo)
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OUTNAME="$RUNNAME"_demux
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#echo "$RUNNAME"
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#echo "$NUMCPU"
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#echo "$OUTNAME"
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# Let guppy do its thing
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guppy_barcoder --input_path "$RUNNAME" --save_path "$OUTNAME" --recursive --records_per_fastq 0 --compress_fastq --worker_threads "$NUMCPU" --device cuda:all:100%
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# Unzip the fastqs
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parallel --gnu -j12 --eta gunzip ::: "$OUTNAME"/*/*.fastq.gz
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# Squish them together
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cat "$OUTNAME"/*/*.fastq > "$OUTNAME"/"$RUNNAME".fastq
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# Rezip the fastqs
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parallel --gnu -j"$NUMCPU" --eta gzip ::: "$OUTNAME"/*/*.fastq
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gzip "$OUTNAME"/"$RUNNAME".fastq
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