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This repository was created with a cookiecutter template, version {{ cookiecutter.template_version }}.

Organization

• The metadata directory contains metadata relevant to annotate the samples.
• The samples.csv file is the master record of all analyzed samples.
• The src directory contains source code used to analyze the data.
• Raw data is under the data directory (likely empty in a remote repository on GitHub).
• Processing of the data creates files under the processed directory.
• Outputs from the analysis are present in the results directory, with subfolders pertaining to each part of the analysis as described below.
• Assembled figures from plots are under the figures directory.
• Manuscript files are under the manuscript directory.

Reproducibility

Running

To see all available steps type:

$ make

Steps used for the initiall processing of raw data are marked with the [dev] label.

Makefile for the {{ cookiecutter.project_slug }} project/package.
Available commands:
help                Display help and quit
requirements        Install Python requirements
process             [dev] Process raw data into processed data types
sync                [dev] Sync data/code to CeMM's cluster
upload_data         [dev] Upload processed files to Zenodo
download_data       Download processed data from Zenodo (for reproducibility)
interactive         [dev] Run an interactive session for analysis
analysis            Run the actual analysis

To reproduce analysis using the pre-preocessed data, one would so:

$ make help
$ make requirements   # install python requirements using pip
$ make download_data  # download data from Zenodo
$ make analysis       # run the analysis scripts

Requirements

• Python 3.10+
• Python packages as specified in the requirements file - install with make requirements or pip install -r requirements.txt.

Virtual environment

It is recommended to use some virtualization or compartimentalization software such as virtual environments or conda to install the requirements.

Here's how to create a virtualenvironment with the repository and installed requirements:

git clone [email protected]:rendeirolab/{{ cookiecutter.project_slug }}.git
cd {{ cookiecutter.project_slug }}
virtualenv .venv
source .venv/bin/activate
pip install -r requirements.txt