This is is the demultiplex pipeline from the Sequana projet
- Overview:
Runs bcl2fastq on raw BCL data and create some QC plots to ease the QC step
- Input:
A valid Illumina base calling directory
- Output:
a set of PNG files and the expected FastQ files
- 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_demultiplex
Usage
sequana_pipelines_demultiplex --help sequana_pipelines_demultiplex --input-directory DATAPATH --run-mode local sequana_pipelines_demutliplex --input-directory DATAPATH --run-mode slurm
This creates a directory fastq. You just need to execute the pipeline:
cd demutliplex sh demutliplex.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the demutliplex.rules and config.yaml files and then execute the pipeline yourself with specific parameters:
snakemake -s demutliplex.rules --cores 4 --stats stats.txt
Or use sequanix interface.
Requirements
This pipelines requires the following executable(s):
bcl2fastq 2.20.0
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.
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