sequana-fastqc

This is is the fastqc pipeline from the Sequana projet

Overview:: Runs fastqc and multiqc on a set of Sequencing data to produce control quality reports
Input:: A set of FastQ files (paired or single-end) compressed or not
Output:: an HTML file index.html (multiqc) and tree.html (individual fastqc report)
Status:: production
Citation:: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352

Installation

You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_fastqc

Usage

sequana_pipelines_fastqc --help
sequana_pipelines_fastqc --input-directory DATAPATH

This creates a directory fastq. You just need to execute the pipeline:

cd fastqc
sh fastqc.sh  # for a local run

This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the fastqc.rules and config.yaml files and then execute the pipeline yourself with specific parameters:

snakemake -s fastqc.rules --cores 4 --stats stats.txt

Or use sequanix interface.

Tutorial

You can retrieve test data from sequana_fastqc (https://github.com/sequana/sequana_fastqc) or type:

wget https://raw.githubusercontent.com/sequana/sequana_fastqc/master/sequana_pipelines/fastqc/data/data_R1_001.fastq.gz
wget https://raw.githubusercontent.com/sequana/sequana_fastqc/master/sequana_pipelines/fastqc/data/data_R2_001.fastq.gz

then, prepare the pipeline:

sequana_fastqc --input-directory .
cd fastqc
sh fastq.sh

# once done, remove temporary files (snakemake and others)
make clean

Just open the HTML entry called index.html and browse the multiqc report. For individual reports, open the tree.html file. You will get expected images such as the following one:

https://github.com/sequana/sequana_fastqc/blob/master/doc/summary.png?raw=true

Requirements

This pipelines requires the following executable(s):

fastqc

https://raw.githubusercontent.com/sequana/sequana_fastqc/master/sequana_pipelines/fastqc/dag.png

Details

This pipeline runs fastqc in parallel on the input fastq files (paired or not) and then execute multiqc. A brief sequana summary report is also produced.

Rules and configuration details

Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.

Changelog

Version	Description
0.9.10	simplify the onsuccess section
0.9.9	add missing png and pipeline (regression bug)
0.9.8	add missing multi_config file
0.9.7	check existence of input directory in main.py add a logo fix schema add multiqc_config add sequana + sequana_fastqc version
0.9.6	add the readtag option

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