millironx/sc2-sequencing
1
0
Fork 0
mirror of https://github.com/MillironX/sc2-sequencing.git synced 2024-12-22 03:08:17 +00:00
Code Issues Releases Packages Activity

Match ONT's nomenclature for fastqs more closely

Browse source
This commit is contained in:
Thomas A. Christensen II 2021-04-22 11:03:21 -06:00
parent ac5be401c1
commit c7545ae55d
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 5 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

7
ont/ont-transfer
View file

@ -72,7 +72,10 @@ mkdir -p "$FASTQPATH"
# Copy the files # Copy the files
for FASTA in ${KEEPERS[@]}; do for FASTA in ${KEEPERS[@]}; do
# Check to see if there are any files here # Check to see if there are any files here
if [[ -n $(find $FOLDERPATH -type f \( -name "*.fast5" -o -name "*.fastq" -o -name "*.fastq.gz" \) -path "*_pass*barcode$FASTA*") ]]; then if [[ -n $(find $FOLDERPATH -type f \( -name "*.fast5" \) -path "*_pass*barcode$FASTA*") ]]; then
# Find the uid that the GridION gives to this sample
ONTID=$(find $FOLDERPATH -name "*.fast5" -path "*_pass*barcode*$FASTA*" | head -n 1 | xargs basename | awk '{split($0,a,"_"); print a[4]}')
# Copy FAST5s # Copy FAST5s
find $FOLDERPATH -name "*.fast5" -path "*_pass*barcode$FASTA*" -exec cp -n {} $FAST5PATH \; find $FOLDERPATH -name "*.fast5" -path "*_pass*barcode$FASTA*" -exec cp -n {} $FAST5PATH \;
@ -80,7 +83,7 @@ for FASTA in ${KEEPERS[@]}; do
find $FOLDERPATH -name "*.fastq.gz" -path "*_pass*barcode$FASTA*" -print0 | xargs -0 -r -L1 -P0 gunzip find $FOLDERPATH -name "*.fastq.gz" -path "*_pass*barcode$FASTA*" -print0 | xargs -0 -r -L1 -P0 gunzip
# Get the name of the resulting FASTQ file # Get the name of the resulting FASTQ file
FASTQRESULT="$FASTQPATH"/"$FOLDERNAME"_pass_barcode"$FASTA".fastq FASTQRESULT="$FASTQPATH"/"$FOLDERNAME"_pass_barcode"$FASTA"_"$ONTID"_0.fastq
# Concatenate the fastqs # Concatenate the fastqs
cat $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq > $FASTQRESULT cat $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq > $FASTQRESULT