jsschrepping/generic-qc repository overview

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.