Development

Replaceable variables in template files

You are going to create many files and scripts for processing and analysis, and many elements in those files can be defined from the configuration files. Making GPM able to handle all these elements is crucial to avoid manual works.

There are two levels of configuration: global and project-wise (see Two levels of configuration files). The way to define them are a bit different:

  • Global configuration (gpm.ini and environment.ini):

    • Just ues the keys in uppercase. This key in your files will be replaced with the corresponding value by GPM.

    • For example, RMD_INSTITUTE_NAME.

  • Project-wise configuration (project.ini):

    • Please add PROJECT_ in front of each key (upper case) defined in gpm/gpm.py.

    • Here is a list of them: date, name1, name2, institute, application, project.ini, project_path, project_name, project_string, bcl_path, demultiplex_path, fastq_path, fastq_multiqc_path, demultiplex_method, processing_path, processing_method, processing_qc_path, organism, genome_assembly, analysis_path, analysis_types, export_URL, export_user, export_password

    • For example, fastq_path should be PROJECT_FASTQ_PATH in your codes.

Please refer to other files in analysis or processing to learn how to use them.

How to add a new demultiplexing method?

When you want to add a new method for demultiplexing, please follow the steps below:

  1. Add a folder under demultiplex/ with a clear and meaningful name. This name must be distinguishable and clear.

  2. Add the template scripts and files into this folder with proper variables. Please refer to Replaceable variables in template files.

  3. Add this method name into GPM_DEMULTIPLEX_METHODS in gpm.ini.

Please test it by gpm demultiplex --help.

How to add a new processing method?

When you want to add a new method for processing the data, please follow the steps below:

  1. Add a folder under processing/ with a clear and meaningful name. This name must be distinguishable and clear.

  2. Add the template scripts and files into this folder with proper variables. Please refer to Replaceable variables in template files.

  3. Add this method name into GPM_PROCESSING_METHODS in gpm.ini.

Please test it by gpm processing --help.

How to add a new analysis?

The analysis feature is controlled by two aspects:

  • What are the relevant files? Rmd? Jupyter-notebook?

  • What is its name and category?

After you can answer the questions above, you can follow the steps below:

  1. Add your files under the category folder in GPM/analysis/.

  2. Define each file in GPM/config/analysis.config.

Please read through Replaceable variables in template files to learn how to utilize the variables managed by GPM.