hic-loop-calling
Detects chromatin loops from Hi-C .mcool files using cooltools, streamlining genomic data analysis for researchers.
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Security score
The hic-loop-calling skill was audited on Feb 9, 2026 and we found 27 security issues across 1 threat category, including 26 high-severity. Review the findings below before installing.
Categories Tested
Security Issues
Template literal with variable interpolation in command context
| 40 | ```bash |
Template literal with variable interpolation in command context
| 76 | 1. Sample name (`sample`): used as prefix and for the output directory `${sample}_loop_calling`. |
Template literal with variable interpolation in command context
| 88 | - Must be the same as the resolution used for `${mcool_uri}` |
Template literal with variable interpolation in command context
| 108 | - Create `${sample}_loop_calling` directory. |
Template literal with variable interpolation in command context
| 109 | - Return the full path of the `${sample}_loop_calling` directory, which will be used as `${proj_dir}`. |
Template literal with variable interpolation in command context
| 121 | - `proj_dir`: directory to save the view file. In this skill, it is the full path of the `${sample}_loop_calling` directory returned by `mcp__project-init-tools__project_init`. |
Template literal with variable interpolation in command context
| 127 | If the conversion is successful, update `${mcool_uri}` to the path of the `.mcool` file. |
Template literal with variable interpolation in command context
| 166 | If the user defined or default `${resolution}` is not found in the list, ask the user to specify the resolution again. |
Template literal with variable interpolation in command context
| 167 | Else, use `${resolution}` for the following steps. |
Template literal with variable interpolation in command context
| 179 | - `proj_dir`: directory to save the expected-cis and eigs-cis files. In this skill, it is the full path of the `${sample}_Compartments_calling` directory returned by `mcp__project-init-tools__project_ |
Template literal with variable interpolation in command context
| 180 | - `mcool_uri`: cooler URI with resolution specified, e.g. `input.mcool::/resolutions/${resolution}` |
Template literal with variable interpolation in command context
| 181 | - `resolution`: `${resolution}` must be the same as the resolution used for `${mcool_uri}` and must be an integer |
Template literal with variable interpolation in command context
| 186 | - If the chromosome names are modified, return the path of the modified .mcool file under `${proj_dir}/` directory |
Template literal with variable interpolation in command context
| 202 | - `mcool_uri`: cooler URI with resolution specified, e.g. `input.mcool::/resolutions/${resolution}` |
Template literal with variable interpolation in command context
| 203 | - `resolution`: `${resolution}` must be the same as the resolution used for `${mcool_uri}` and must be an integer |
Template literal with variable interpolation in command context
| 204 | - `proj_dir`: directory to save the view file. In this skill, it is the full path of the `${sample}_loop_calling` directory returned by `mcp__project-init-tools__project_init`. |
Template literal with variable interpolation in command context
| 210 | - Return the path of the view file under `${proj_dir}/temp/` directory. |
Template literal with variable interpolation in command context
| 224 | - `proj_dir`: directory to save the view file. In this skill, it is the full path of the `${sample}_loop_calling` directory returned by `mcp__project-init-tools__project_init`. |
Template literal with variable interpolation in command context
| 225 | - `mcool_uri`: cooler URI with resolution specified, e.g. `input.mcool::/resolutions/${resolution}` |
Template literal with variable interpolation in command context
| 226 | - `resolution`: `${resolution}` must be the same as the resolution used for `${mcool_uri}` and must be an integer |
Template literal with variable interpolation in command context
| 227 | - `view_path`: the path to the view file (e.g. `${proj_dir}/temp/view_${genome}.tsv`) |
Template literal with variable interpolation in command context
| 233 | - Return the path of the expected cis file under `${proj_dir}/temp/` directory. |
Template literal with variable interpolation in command context
| 246 | - `proj_dir`: directory to save the view file. In this skill, it is the full path of the `${sample}_loop_calling` directory returned by `mcp__project-init-tools__project_init`. |
Template literal with variable interpolation in command context
| 247 | - `mcool_uri`: cooler URI with resolution specified, e.g. `input.mcool::/resolutions/${resolution}` |
Template literal with variable interpolation in command context
| 248 | - `resolution`: `${resolution}` must be the same as the resolution used for `${mcool_uri}` and must be an integer |
Template literal with variable interpolation in command context
| 249 | - `view_path`: the path to the view file (e.g. `${proj_dir}/temp/view_${genome}.tsv`) |
Template literal with variable interpolation in command context
| 255 | - Return the path of the loops bedpe file under `${proj_dir}/loops/` directory. |