hic-normalization
Automates the detection and normalization of Hi-C data in .cool and .mcool formats, ensuring data is ready for analysis.
Install this skill
Security score
The hic-normalization skill was audited on Feb 9, 2026 and we found 7 security issues across 1 threat category, including 6 high-severity. Review the findings below before installing.
Categories Tested
Security Issues
Template literal with variable interpolation in command context
| 37 | ```bash |
Template literal with variable interpolation in command context
| 50 | 1. Sample name (`sample`): used as prefix and for the output directory `${sample}_hic_norm`. |
Template literal with variable interpolation in command context
| 71 | - Create `${sample}_hic_norm` directory. |
Template literal with variable interpolation in command context
| 72 | - Get the full path of the `${sample}_hic_norm` directory, which will be used as `${proj_dir}`. |
Template literal with variable interpolation in command context
| 84 | - `proj_dir`: directory to save the view file. In this skill, it is the full path of the `${sample}_hic_norm` directory returned by `mcp__project-init-tools__project_init`. |
Template literal with variable interpolation in command context
| 91 | If the conversion is successful, update `${mcool_uri}` to the path of the `.mcool` file. The `${mcool_path}` should be updated to the path of the `.mcool` file without resolution specified. |
Template literal with variable interpolation in command context
| 130 | - Return the path of the balanced .mcool file under `${proj_dir}/` directory. |