2021-03-26 20:08:34 +00:00
|
|
|
#!/bin/bash
|
|
|
|
|
# Combines the output from the ONT GridION into a single compressed fastq file
|
|
|
|
|
|
|
|
|
|
# Initiation, get some important info
|
|
|
|
|
RUNNAME=$(basename "${1}")
|
|
|
|
|
NUMCPU=$(grep -c processor < /proc/cpuinfo)
|
|
|
|
|
OUTNAME="$RUNNAME"_demux
|
|
|
|
|
|
|
|
|
|
#echo "$RUNNAME"
|
|
|
|
|
#echo "$NUMCPU"
|
|
|
|
|
#echo "$OUTNAME"
|
|
|
|
|
|
|
|
|
|
# Let guppy do its thing
|
|
|
|
|
guppy_barcoder --input_path "$RUNNAME" --save_path "$OUTNAME" --recursive --records_per_fastq 0 --compress_fastq --worker_threads "$NUMCPU" --device cuda:all:100%
|
|
|
|
|
|
|
|
|
|
# Unzip the fastqs
|
2021-03-30 14:52:23 +00:00
|
|
|
parallel --gnu -j"$NUMCPU" --eta gunzip ::: "$OUTNAME"/*/*.fastq.gz
|
2021-03-26 20:08:34 +00:00
|
|
|
|
|
|
|
|
# Squish them together
|
|
|
|
|
cat "$OUTNAME"/*/*.fastq > "$OUTNAME"/"$RUNNAME".fastq
|
|
|
|
|
|
|
|
|
|
# Rezip the fastqs
|
|
|
|
|
parallel --gnu -j"$NUMCPU" --eta gzip ::: "$OUTNAME"/*/*.fastq
|
|
|
|
|
gzip "$OUTNAME"/"$RUNNAME".fastq
|
