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Fix fast5 detection

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This commit is contained in:
Thomas A. Christensen II 2021-03-23 12:21:38 -06:00
parent 03934e8144
commit 1a560be81a
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 4 additions and 4 deletions
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8
ont/ont-transfer.sh
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@ -15,7 +15,7 @@ fi
# Find the directory we are supposed to copy
# If no directory was passed, check to see if the current directory will work
if [ "$FOLDERIN" = "" ]; then
if [ -d "fast5_pass" ]; then
if [[ -n $(find . -type d -name "fast9_pass") ]]; then
FOLDERPATH="$PWD"
FOLDERNAME=$(basename "$PWD")
else
@ -61,9 +61,9 @@ mkdir -p "$USBDRIVE/$FOLDERNAME/fastq"
# Copy the files
for FASTA in "${KEEPERS[@]}"; do
cp -n $FOLDERPATH/fast5_pass/barcode$FASTA/*.fast5 $USBDRIVE/$FOLDERNAME/fast5 2> /dev/null
cp -n $FOLDERPATH/fastq_pass/barcode$FASTA/*.fastq $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null
cp -n $FOLDERPATH/fastq_pass/barcode$FASTA/*.fastq.gz $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null
cp -n $FOLDERPATH/*/fast5_pass/barcode$FASTA/*.fast5 $USBDRIVE/$FOLDERNAME/fast5 2> /dev/null
cp -n $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null
cp -n $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq.gz $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null
done
# Make sure we end on a happy note, regardless if there were actually 96 barcodes