From 1a560be81a04b3af12301aec55b5305c2e0fa1f5 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 23 Mar 2021 12:21:38 -0600
Subject: [PATCH] Fix fast5 detection

---
 ont/ont-transfer.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/ont/ont-transfer.sh b/ont/ont-transfer.sh
index fa3988d..fa2d90b 100755
--- a/ont/ont-transfer.sh
+++ b/ont/ont-transfer.sh
@@ -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