Update README.md

README.md

@@ -15,19 +15,10 @@ mcmicro nf-core module for cell phenotyping using CELESTA
 - If optional vector inputs are not given, a custom vector is created that consists of only 1s
 - Checking if folder output and a title were provided
 - Surpressing the default `save_result` output from `AssignCells()`
-- Creating the desired CSV output by getting `final_cell_tyoe_assignment`, `coords`and `marker_exp_prob` from the `CelestaObj`
+- Creating the desired CSV output by getting `final_cell_type_assignment`, `coords`and `marker_exp_prob` from the `CelestaObj`
 
 ### How to use CELESTA_CLI
 
-- `-i`/`--image_data` which should provide the path to the quantification output as a .csv (e.g. after running MCMICRO). The file should include marker intensities, CellID and X/Y columns. This input is mandatory.
-- `-s`/`--signature` which shoould provide the path to the signature matrix for cell type definition (also known as prior marker info) as a .csv file. Description found here [CELESTA](https://github.com/plevritis-lab/CELESTA). This input is mandatory.
-- `--anchor_high` which should provide the path to a 1 row .csv file (i.e. a vector) to define high thresholds for anchor cell identification. Examples can be found [here](https://github.com/plevritis-lab/CELESTA/tree/main/data). This input is mandatory.
-- `--index_high`which should provide the path to a 1 row .csv file (i.e. a vector) to define high thresholds for index cell identification during iteration. Examples can be found [here](https://github.com/plevritis-lab/CELESTA/tree/main/data). This input is mandatory.
-- `--anchor_low` which should provide the path to a 1 row .csv file (i.e. a vector) to define low thresholds for anchor cell identification. Examples can be found [here](https://github.com/plevritis-lab/CELESTA/tree/main/data). This input is optional. If not provided, a vector consisting of only `1`, with length equal to input from `--anchor_high`, will be created.
-- `--index_low`which should provide the path to a 1 row .csv file (i.e. a vector) to define low thresholds for index cell identification during iteration. Examples can be found [here](https://github.com/plevritis-lab/CELESTA/tree/main/data). This input is optional. If not provided, a vector consisting of only `1`, with length equal to input from `--anchor_high`, will be created.
-- `-o`/`--output`, which should provide the path to the output folder. This input is optional. If not provided, the current working directory will be used.
-- `-t`/`--title`, which should be a user-defined tag that will be used to define the project title inside the CELESTA algorithm and will be provided in the result .csv file
-
 | Option         | Description                                                                                                                                                         | Mandatory |
 |----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
 | -i/--image_data| Path to the quantification output as a .csv (e.g., after running MCMICRO). Includes marker intensities, CellID, and X/Y columns.                                      | Yes       |