Snakemake workflow used to control read qualities over fastq files with FastQC.
This pipeline is meant to be used in teaching sessions or imported in other snakemake-workflows.
The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.
A complete description of the results can be found here in workflow reports.
The tools used in this pipeline are described here textually.
┌────────────────────────┐
│ Copy / Link / Concat │
└─┬───────────────────┬──┘
│ │
┌────────▼─┐ ┌───▼────────────┐
│ │ │ │
│ FastQC │ │ FastQ-Screen │
│ │ │ (Optional) │
└─────┬────┘ └─────┬──────────┘
│ │
│ │
│ ┌───────────┐ │
│ │ │ │
└─────► MultiQC ◄──────┘
│ │
└───────────┘
| Step | Wrapper |
|---|---|
| FastQC | fastqc-wrapper |
| FastScreen | fastq-screen |
| MultiQC | multiqc-wrapper |