dissectBCL

Demultiplexing pipeline for illumina data (novaseq/miseq/nextseq). Continuation of Devon Ryan's TWTWTWTW.

Installation.

Clone this repository, create the environment and pip install

git clone git@github.com:maxplanck-ie/dissectBCL.git
cd dissectBCL
conda env create -f env.yml --name dissectBCL
conda activate dissectBCL
pip install ./

Note

If you get LookupError: setuptools-scm was unable to detect version. Ensure that git is available on the conda environment you've just activated: conda install git.

Running.

Fill in the dissectBCL.ini file appropriately. By default the config file is expected to be in ~/configs/dissectBCL_prod.ini.

dissect

or

dissect -c /path/to/config.ini

or

dissect -f /path/to/flowcell.ini

Docs.

Documentation is available here.