Checklists generator

Python script to dynamically generate the bioinfo production checklists for QC, Delivery and Close of NGI sequencing projects. The script uses Quarto to generate the checklists in HTML or markdown format. The checklists are based on templates that can be customized to fit the needs of different projects.

The templates are based on the following internal documents and versions:

• Bioinfo QC: 1617:4
• Delivery: 1286:22
• Close: 1262:17

Requirements

• Python 3.10 or higher
• Quarto installed

Usage

Clone the repository and run the following minimal command in the root directory:

python generate_checklists.py --output-path . --format html

This will generate three checklists (i.e. QC, Delivery and Close) in HTML format in the current directory. It will also generate the corresponding .qmd files with the same base name, and place them in the qmds folder. A .qmd file is a Quarto document that can be edited and rendered to generate a new HTML file with the updated checklist.

To re-generate any of the checklists after having modified its .qmd file, run the following command:

quarto render qmds/<qmd_file> --to html --embed-resources --standalone

Instead, if you want to generate the checklists in markdown format, run:

quarto render qmds/<qmd_file> --to markdown --embed-resources --standalone

Options

• --help: Show the help message and exit.
• --templates-path: The path to the template files. The default is templates. The script will look for three files in this directory: QC_template.qmd, Delivery_template.qmd, and Close_template.qmd. These files are used to generate the QC checklist, delivery checklist, and close checklist, respectively.
• --format: The output format for the checklist. The default is markdown. The other option is html. If markdown is selected, the script can make use of the md_path option to save the markdown file in a specific location.
• --project: The project ID for which the QC checklist will be generated. If not provided, the script will leave a generic placeholder (<project_id>) in the output file.
• --flowcell: The flowcell ID for the project. If not provided, the script will leave a generic placeholder (<flowcell_id>) in the output file.
• --author: The full name of the author. If not provided, the script will not include the author in the output file.
• --email: The email address of the author. If not provided, the script will not include the email in the output file.
• --ngi-path: The path to the NGI folder on Miarka. This is used to generate the path to the project folders. If not provided, the script will leave a generic placeholder (<ngi_path>) in the output file.
• --config-path: The path to the TACA configuration folder. This is used to generate the path to the project folders. If not provided, the script will leave a generic placeholder (<config_path>) in the output file.
• --genstat-url: The URL for the Genomics Status page. If not provided, the script will leave a generic placeholder (<genstat_url>) in the output file.
• --charon-url: The URL for the Charon page. If not provided, the script will leave a generic placeholder (<charon_url>) in the output file.
• --quarto-path: The path where the Quarto file will be saved. The default is /usr/local/bin/quarto. If the executable is not found, the script will attempt to search for it in the system path.
• --output-path: The directory where the output files will be saved. The default is the current directory.
• --timestamp: Whether to include a timestamp in the output file name. The default is False. If True, the output file will be named <timestamp>_<project_id>_QC_checklist.html or <timestamp>_<project_id>_QC_checklist.md. The timestamp format is YYYYMMDD.
• --output-structure: The structure of the output. The default is flat. The other option is nested. If nested is selected, the output files will be saved in a subdirectory named after the project ID.
• --force: Force overwrite of existing files. If not provided and the output file already exists, the script will not overwrite it and will exit with an error message.
• --log-level: The logging level. The default is INFO. Other options are DEBUG, WARNING, ERROR, and CRITICAL. This can be set to DEBUG for more detailed logging information.

Configuration file

If a config.json file is present in the same directory as the script, it will be used to set the default values for all or some of the options. The configuration file should be in JSON format and can include the following keys:

• templates_path [string]
• format [string]
• project [string]
• flowcell [string]
• author [string]
• email [string]
• ngi_path [string]
• config_path [string]
• genstat_url [string]
• charon_url [string]
• quarto_path [string]
• output_path [string]
• timestamp [bool]
• output_structure [string]
• force [bool]
• log_level [string]

Note: The base working path on Miarka and the URLs for Genomics Status and Charon have been replaced with generic placeholders (<ngi_path>, <genstat_url>, and <charon_url>) in the template files. This was done to avoid hardcoding sensitive information in the script and templates. Therefore, it is highly recommended to set these values in the local configuration file or pass them as command line arguments when running the script. The script will use the provided values to replace the placeholders in the template files before generating the final outputs.

Example of config.json file:

{
  "author": "John Doe",
  "email": "[email protected]",
  "format": "markdown",
  "output_path": "/path/to/output/directory",
  "output_structure": "nested",
  "quarto_path": "/usr/local/bin/quarto",
  "ngi_path": "/path/to/NGI/folder",
  "genstat_url": "https://genstat.example.com",
  "charon_url": "https://charon.example.com",
  "config_path": "/path/to/conf/TACA"
}