Push the button, you won't believe what will happen next.

Mundanity, managed

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"The Big Red Button" is a program for automated analysis of demultiplexed datasets. It ties in with other solutions that we've created and use to provide a complete loop from sample submission to returned QC metrics.

The general steps of the BigRedButton pipeline (in python, the BRB or "be right back" module) are as follows:

1. Read in the configuration file (~/BigRedButton.ini and reimport the package).
2. Check for newly finished demultiplexing runs (BRB.findFinishedFlowcells()). If there are none, then sleep.
3. For each newly demultiplexed run, contact Parkour to get the library types and organisms per library/sample.
4. Filter the Parkour results for what can currently be processed (see ~/BigRedButton.ini).
5. Run an appropriate Snakepipe.
6. Send QC information back to Parkour (BRB.ET.phoneHome()).
7. Mark a flow cell as finished by touching analysis.done.

An analysis can be rerun by deleting analysis.done in the folder holding the demultiplexed results. The actual output is written only in the group directories (specifically, their sequencing_data directories).

The pipeline can be woken from sleep by sending it a HUP signal (e.g., killall -HUP BigRedButton.py).

The configuration file in the source directory should be copied to your home directory and modified to suite your needs (see the documentation in the file). Also, you should run nohup BigRedButton.py & to start the pipeline, so it continues after you log out.

Installation

conda create -n BRB python -y
conda activate BRB
git clone git@github.com:maxplanck-ie/BigRedButton.git
cd BigRedButton
pip install .

Additional tools

1. BRB expects snakePipes is already installed and defined in the config file
2. In adition, it expects the 10X_snakepipe repository also defined in the config file