Given /input directory of the form
input
├── run1
│ ├── {sample1}_001.fastq.gz
│ ├── {sample1}_002.fastq.gz
│ └── {sample1}_003.fastq.gz
└── run2
├── {sample2}_001.fastq.gz
├── {sample2}_002.fastq.gz
└── {sample3}_001.fastq.gz
does the following.
For each directory (run1, run2) merge all files differing only by
the last three digits (_001.fastq.gz, _002.fastq.gz, ...) and run
fastqc on them. Then combine the qc from all the files into one
report with multiqc and place the results in /output.