An "experiment" here refers to a computational experiment, two experiments could be two different processings of the same raw data, or to the same processing of two different datasets.

• bin folder: contains the scripts for each experiments.
• submit_HPC_slurm folder: contains the SBATCH scripts to submit the scripts in bin to the Slurm workload manager of the HPC.
• data folder: contains symbolic links to the RDS (where the raw sequencing data is) and to scratch directory (where the results, including intermediates, are stored for each experiment).
• params_bioinfo_experiments folder: contains the parameter file with explanations of processing steps for each experiment. The relevant parameter file is sourced by params_bioinfo_experiments/0_params.sh0_params.sh.
• temp_logs: temporary location for log files before they are automatically moved to the log directory of the running experiment (unless a certain kind of error occurs).
• notebooks folder: contains the Jupyter / RMarkdown notebooks for tbe downstream analysis of each experiment.
• resources folder: contains various resources, e.g., protocol cell barcodes.
• misc folder: miscellaneous items.