schultzelab/generic-qc repository overview

Given /input directory of the form

input
├── xxx
│   ├── 3651_ATTCCT_L002_R1_001.fastq.gz
│   ├── 3651_ATTCCT_L002_R1_002.fastq.gz
│   └── 3651_ATTCCT_L002_R1_003.fastq.gz
└── yyy
    ├── 3652_ACTGAT_L002_R1_001.fastq.gz
    ├── 3652_ACTGAT_L002_R1_002.fastq.gz
    └── 3652_ACTGAT_L002_R1_003.fastq.gz

does the following.

For each directory (xxx, yyy) 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.