diff --git a/README.md b/README.md index efb477c..f11e9dc 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ mcmicro nf-core module for cell phenotyping using CELESTA - Surpressing the default `save_result` output from `AssignCells()` - Creating the desired CSV output by getting `final_cell_type_assignment`, `coords`and `marker_exp_prob` from the `CelestaObj` -### How to use CELESTA_CLI +### Usage | Option | Description | Mandatory | |----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------| @@ -29,3 +29,10 @@ mcmicro nf-core module for cell phenotyping using CELESTA | --index_low | Path to a 1 row .csv file (i.e., a vector) defining low thresholds for index cell identification during iteration. Examples can be found [here](https://example.com). | No | | -o/--output | Path to the output folder. If not provided, the current working directory will be used. | No | | -t/--title | User-defined tag used to define the project title inside the CELESTA algorithm and provided in the result .csv file. | No | + +### Docker Usage + +To build the container: +``` +git clone +```