Merge fastq.gz files with same name in different localizations in Google-Cloud - bash

Question

I would like to merge several fastq.gz files with the same name in different folders in the Google-Cloud. I have a total of 15 patients. Each patient has paired-end data "R1" and "R2". Each R1 and R2 are divided into 4 files. The size of each file is approximately 28 GB.
My goal is to merge the 4 files to obtain the complete fastq.gz R1 and R2 files for each patient.
I have never worked with Google-Cloud before.
Here is how the folders and the files are in the bucket (example with 2 patients):
gs://bucketID
/folder1
/folder001
Patient1_R1.fastq.gz
Patient1_R2.fastq.gz
/folder002
Patient2_R1.fastq.gz
Patient2_R2.fastq.gz
etc.
/folder2
/folder003
Patient1_R1.fastq.gz
Patient1_R2.fastq.gz
/folder004
Patient2_R1.fastq.gz
Patient2_R2.fastq.gz
etc.
/folder3
/folder005
Patient1_R1.fastq.gz
Patient1_R2.fastq.gz
/folder006
Patient2_R1.fastq.gz
Patient2_R2.fastq.gz
etc.
/folder4
/folder007
Patient1_R1.fastq.gz
Patient1_R2.fastq.gz
/folder008
Patient2_R1.fastq.gz
Patient2_R2.fastq.gz
etc.
I want to make a script that targets fastq.gz files with the same name in different folders, then merge them. However, I have no idea how to do this on Google-Cloud.
Here is the same example with colors (I want to concatenate files with the same color):
Example with colors
Here's how I see the bash script:
bucket="bucketID"
dir1=$bucket/"folder1"
dir2=$bucket/"folder2"
dir3=$bucket/"folder3"
dir4=$bucket/"folder4"
destdir=$bucket/"destdir"
participants = (Patient1
Patient2
)
for i in ${participants[*]};
do
zcat dir1/.../$i/_R1.fastq.gz dir2/.../$i/_R1.fastq.gz dir3/.../$i/_R1.fastq.gz dir4/.../$i/_R1.fastq.gz | gzip >$destdir/"merged_"$i/_R1.fastq.gz
zcat dir1/.../$i/_R2.fastq.gz dir2/.../$i/_R2.fastq.gz dir3/.../$i/_R2.fastq.gz dir4/.../$i/_R2.fastq.gz | gzip >$destdir/"merged_"$i/_R2.fastq.gz
done
Should I use "gsutil compose" instead to merge?
At the end, I would like to have only two files R1 and R2 for each patient: merged_patient#_R1.fastq.gz and merged_patient#_R2.fastq.gz.
In the example I gave above, it would give 4 files:
merged_Patient1_R1.fastq.gz
merged_Patient1_R2.fastq.gz
merged_Patient2_R1.fastq.gz
merged_Patient2_R2.fastq.gz
Thank you!

Answer 1

I would recommend you to use the following command in order to concatenate your files:
gsutil compose gs://bucket/obj1 [gs://bucket/obj2 ...] gs://bucket/composite
You can check the documentation in this link.
I've tried to do a simple bash script by using the "gsutil compose" command with fastq.gz files, and it was working fine for me.
The compose command creates a new object whose content is the concatenation of a given sequence of source objects under the same bucket.
Hope this helps!

Answer 2

Ok I found the solution with gsutil compose :
declare -a participantsArray=("Patient1"
"Patient2"
)
bucket="bucketID"
dir1=$bucket/"folder1"
dir2=$bucket/"folder2"
dir3=$bucket/"folder3"
dir4=$bucket/"folder4"
destdir=$bucket/"destdir"
for i in ${participantsArray[#]};
do
fileR1="${i}_R1.fastq.gz"
fileR2="${i}_R2.fastq.gz"
gsutil compose "${dir1}/*/${fileR1}" "${dir2}/*/${fileR1}" "${dir3}/*/${fileR1}" "${dir4}/*/${fileR1}" "${destdir}/merged_${fileR1}"
gsutil compose "${dir1}/*/${fileR2}" "${dir2}/*/${fileR2}" "${dir3}/*/${fileR2}" "${dir4}/*/${fileR2}" "${destdir}/merged_${fileR2}"
done
As you said the solution was not difficult to find.
Thank you again!