Report Generator CLI

Overview

This project provides a command line interface for generating reports from a Kraken-style Bracken abundance table. The reports are generated using templates and can be customized based on participant data. This package was made for a project in the Elinav Lab (Weizmann Institute of Science, DKFZ Heidelberg).

Installation

To install the CLI, follow these steps:

1. Download or clone the repository to your local directory.

2. Run the setup script to install the CLI. You can run the script without any arguments to install it to the default directory (~/bin), or specify a custom directory.

sh sh setup.sh

Or, to specify a custom directory:

sh sh setup.sh /path/to/custom/dir

1. Ensure the target directory is in your PATH. When prompted by the script, say 'yes' if you want the report generator to be available in your path. Otherwise manually: If you installed the CLI to ~/bin, add the following line to your shell profile (e.g., .bashrc), followed by a command to reload your shell profile:

sh export PATH="$HOME/bin:$PATH" source ~/.bashrc If you specified a custom directory, replace ~/bin with your custom directory path.

1. Verify the installation by running the reportgenerator command:

sh reportgenerator --help

This should display the help message for the reportgenerator script, confirming that the installation was successful.

Dependencies

System Requirements

• R (version 4.0 or higher)
• Quarto (version 1.3 or higher)
• Bash shell environment

R Packages

The following R packages will be automatically installed if missing:

Core packages: - dplyr: For data manipulation - stringr: For string handling - ggplot2: For generating visualizations - optparse: For command line argument parsing - forcats: For factor level manipulation - tidyr: For data reshaping

Test packages (only needed when running tests): - testthat: For unit testing - mockery: For mocking in tests - R6: For test reporter classes

All required R packages are automatically installed when first running the tool. If you prefer to install them manually:

```r

Install core packages

install.packages(c("dplyr", "stringr", "ggplot2", "optparse", "forcats", "tidyr"))

Install test packages (optional)

install.packages(c("testthat", "mockery", "R6")) ```

Usage

To generate a report, use the reportgenerator command followed by the necessary arguments. For example:

sh reportgenerator -a input_file -o output_dir

For more information on the available options and arguments, run:

sh reportgenerator --help Running tests: bash reportgenerator --test The test uses an example minimal abudance table from the testfolder of the package.

Command Line Options

| Option | Description | Required? | Default | |--------|-------------|-----------|---------| | -a, --abundance | Path to abundance table file | REQUIRED | - | | -p, --template | Path to report template | Optional | templates/reporttemplate.qmd | | -i, --infosheet | Path to physician info template | Optional | templates/physicianinfo_template.qmd | | -o, --output | Output directory for reports | Optional | reports | | -s, --sample | Sample prefix in column names | Optional | Sample | | -t, --test | Run tests instead of normal operation | Optional | FALSE |

Input Format

The abundance table should be a tab-delimited file with the following format: - First column: Taxonomic name - Second column: Taxonomic rank (D, P, C, O, F, G, S) - Remaining columns: Sample abundances with names like Sample001.kraken2.report_bracken

Output

The tool generates: - Individual PDF reports for each sample in the abundance table - A general information sheet (physician_info.pdf) - All files are saved to the specified output directory

HPC Usage

When using on an HPC system, you may need to load the required modules: bash module load R module load quarto Or activate a mamba environment with the dependencies needed for this tool.

Development

To modify templates, edit files in the templates/ directory.

Contributing

Contributions are welcome! Please feel free to submit a pull request or open an issue for any enhancements or bug fixes.

License

This project is licensed under the MIT License. See the LICENSE file for details.