sequana-fastqc 1.0.1

Installation

You must install Sequana first (use –upgrade to get the latest version installed):

pip install sequana --upgrade

Then, just install this package:

pip install sequana_fastqc --upgrade

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.

Please see the Wiki for more examples and features.

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 summary.html. A multiqc report is also available. You will get expected images such as the following one:

Please see the Wiki for more examples and features.

Requirements

This pipelines requires the following executable(s):

• fastqc

For Linux users, we provide a singularity image available through damona:

pip install damona
damona install fastqc
# and add the ~/.config/damona/bin path to your binary PATH

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

Contribute & Code of Conduct

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.