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Fix hardcoded task number to unzip fastqs

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Thomas A. Christensen II 2021-03-30 08:52:23 -06:00 committed by GitHub
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@ -14,7 +14,7 @@ OUTNAME="$RUNNAME"_demux
guppy_barcoder --input_path "$RUNNAME" --save_path "$OUTNAME" --recursive --records_per_fastq 0 --compress_fastq --worker_threads "$NUMCPU" --device cuda:all:100% guppy_barcoder --input_path "$RUNNAME" --save_path "$OUTNAME" --recursive --records_per_fastq 0 --compress_fastq --worker_threads "$NUMCPU" --device cuda:all:100%
# Unzip the fastqs # Unzip the fastqs
parallel --gnu -j12 --eta gunzip ::: "$OUTNAME"/*/*.fastq.gz parallel --gnu -j"$NUMCPU" --eta gunzip ::: "$OUTNAME"/*/*.fastq.gz
# Squish them together # Squish them together
cat "$OUTNAME"/*/*.fastq > "$OUTNAME"/"$RUNNAME".fastq cat "$OUTNAME"/*/*.fastq > "$OUTNAME"/"$RUNNAME".fastq