This is is the demultiplex pipeline from the Sequana projet
- Overview:
Runs bcl2fastq on raw BCL data and creates plots to ease the QC validation
- Input:
A valid Illumina base calling directory
- Output:
a set of PNG files and the expected FastQ files
- Status:
production
- Wiki:
- Documentation:
This README file, the Wiki from the github repository (link above) and sequana.readthedocs.io
- 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 --working-directory DATAPATH --bcl-directory bcldata --samplesheet SampleSheet.csv
This creates a directory fastq. You just need to execute the pipeline:
cd demultiplex sh demultiplex.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the demultiplex.rules and config.yaml files and then execute the pipeline yourself with specific parameters:
snakemake -s demultiplex.rules --cores 4 --stats stats.txt
Or use sequanix interface.
Would you need to merge the lane, please add the –merging-strategy argument followed by merge:
sequana_pipelines_demultiplex --bcl-directory bcl_data --merging-strategy merge
Requirements
This pipelines requires the following executable(s):
bcl2fastq 2.20.0
bcl2fastq should be present in your path. Most facilities have the tools installed. On cluster, modules provide the tool as well. If you do not have it, we provide a singularity image, which can be download as follow:
singularity pull bcl2fastq.img shub://cokelaer/ngstools:bcl2fastq
Then, just add a script called bc2fastq in your binary PATH with is content:
singularity run PATH_TO_image/bcl2fastq.img ${1+"$@"}
Details
This pipeline runs bcl2fastq 2.20 and creates a set of diagnostics plots to help deciphering common issues such as missing index and sample sheet errors.
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 |
|---|---|
0.9.11 |
|
0.9.10 |
|
0.9.9 |
|
0.9.8 |
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0.9.7 |
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0.9.6 |
|
0.9.5 |
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0.9.4 |
|
0.9.3 |
Fix regression bug |
0.9.2 |
remove warning due to relative paths. |
0.9.1 |
Make the merging options compulsory. Users must tell whether they want to merge the lanes or not. This avoid to do the merging or not whereas the inverse was expected. |
0.8.6 |
Uses 64G/biomics queue and 16 cores on a SLURM scheduler |
1 maintainer
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