README.md

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.

Usage

The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.

Results

A complete description of the results can be found here in workflow reports.

Material and Methods

The tools used in this pipeline are described here textually.

       ┌────────────────────────┐
       │  Copy / Link / Concat  │
       └─┬───────────────────┬──┘
         │                   │
┌────────▼─┐             ┌───▼────────────┐
│          │             │                │
│  FastQC  │             │  FastQ-Screen  │
│          │             │   (Optional)   │
└─────┬────┘             └─────┬──────────┘
      │                        │
      │                        │
      │     ┌───────────┐      │
      │     │           │      │
      └─────►  MultiQC  ◄──────┘
            │           │
            └───────────┘

QC

Step	Wrapper
FastQC	fastqc-wrapper
FastScreen	fastq-screen
MultiQC	multiqc-wrapper