Loops in bash to organise fastqs - bash

Question

I have a problem which I think needs loops to solve.
I have fastq files that follow the naming conventions, all in a generic directory e.g 'allpools' :
ls allpools
2022_pool_1_Seq_GEX.fastq.gz
2022_pool_1_Seq_CMO.fastq.gz
2022_pool_2_Seq_GEX.fastq.gz
2022_pool_2_Seq_CMO.fastq.gz
I need one loop to make directories in 'allpools' for as many pool numbers as there are in the fastqs, where the resulting directories will be called :
pool1
pool2
and then another loop whereby the original fastqs are moved and placed in respective directories for gex and cmo. As an example :
allpools/pool1/pool1_GEX #containing all gex fastqs of pool_1
allpools/pool1/pool1_CMO #containing all cmo fastqs of pool_1
####
allpools/pool2/pool2_GEX #containing all gex fastqs of pool_2
allpools/pool2/pool2_CMO #containing all cmo fastqs of pool_2

Answer 1

Before:
$ tree allpools/
allpools/
├── 2022_pool_1_Seq_CMO.fastq.gz
├── 2022_pool_1_Seq_GEX.fastq.gz
├── 2022_pool_2_Seq_CMO.fastq.gz
└── 2022_pool_2_Seq_GEX.fastq.gz
Use sed to parse the filename and generate the directory name:
$ for f in allpools/*; do d=$(sed -E 's%.+(pool_[0-9]+).+(GEX|CMO).+%\1/\1_\2%' <<<$f); mkdir -p allpools/$d; mv -vi $f allpools/$d/; done
renamed 'allpools/2022_pool_1_Seq_CMO.fastq.gz' -> 'allpools/pool_1/pool_1_CMO/2022_pool_1_Seq_CMO.fastq.gz'
renamed 'allpools/2022_pool_1_Seq_GEX.fastq.gz' -> 'allpools/pool_1/pool_1_GEX/2022_pool_1_Seq_GEX.fastq.gz'
renamed 'allpools/2022_pool_2_Seq_CMO.fastq.gz' -> 'allpools/pool_2/pool_2_CMO/2022_pool_2_Seq_CMO.fastq.gz'
renamed 'allpools/2022_pool_2_Seq_GEX.fastq.gz' -> 'allpools/pool_2/pool_2_GEX/2022_pool_2_Seq_GEX.fastq.gz'
After:
$ tree allpools/
allpools/
├── pool_1
│   ├── pool_1_CMO
│   │   └── 2022_pool_1_Seq_CMO.fastq.gz
│   └── pool_1_GEX
│   └── 2022_pool_1_Seq_GEX.fastq.gz
└── pool_2
├── pool_2_CMO
│   └── 2022_pool_2_Seq_CMO.fastq.gz
└── pool_2_GEX
└── 2022_pool_2_Seq_GEX.fastq.gz