update docs

Author: FlorianBarkmann

README.md

@@ -20,7 +20,7 @@ conda activate cansig
 ### Data Preparation
 
 After setting up the environment, you'll need to download the cancer datasets from the Curated Cancer Cell Atlas (CCCA). These datasets form the foundation for the benchmarking analysis.
-For detailed instructions on downloading and processing the CCCA datasets, see the [CCCA Data Download Guide](ccca.md).
+For detailed instructions on downloading and processing the CCCA datasets, see the [CCCA Data Download Guide](https://boevalab.github.io/CanSig-benchmark/ccca.html).
 
 Quick start for downloading a test dataset:
 

docs/source/getting_started.md

@@ -46,12 +46,12 @@ To reproduce the specific results from the CanSig-benchmark paper, use the provi
 
 **Signature Analysis Pipeline:**
 ```bash
-snakemake --configfile config/signatures/<config>.yaml --sdm apptainer --apptainer-args "\\-\\-nvccli" -c <number_of_cores> -s signatures.smk
+snakemake --configfile configs/signatures/<config>.yaml --sdm apptainer --apptainer-args "\\-\\-nvccli" -c <number_of_cores> -s signatures.smk
 ```
 
 **Integration Analysis Pipeline:**
 ```bash
-snakemake --configfile config/integration/<config>.yaml --sdm apptainer --apptainer-args "\\-\\-nvccli" -c <number_of_cores> -s integration.smk
+snakemake --configfile configs/integration/<config>.yaml --sdm apptainer --apptainer-args "\\-\\-nvccli" -c <number_of_cores> -s integration.smk
 ```
 
 Replace `<config>` with the specific configuration file name you want to use. The `--nvccli` argument enables NVIDIA container support for GPU-accelerated methods.

docs/source/tutorials/data.md

@@ -71,26 +71,32 @@ conda activate cansig
    snakemake --configfile your_config.yml --sdm apptainer -c <number-of-cores> -s integration.smk
    ```
 
-   **For both (complete pipeline):**
-   ```bash
-   snakemake --configfile your_config.yml --sdm apptainer -c <number-of-cores>
-   ```
-
 Replace `<number-of-cores>` with the number of CPU cores you want to allocate to the pipeline.
 
 
 ## Output Structure
 
 Results will be organized in your specified directory as follows:
 ```
+# For -s signatures.smk
 results/your_analysis/
 ├── benchmarks/     # Performance benchmarks for each pipeline step
 ├── corrs/          # Correlation analysis results
 ├── data/           # Processed data files
 ├── integration/    # Integrated datasets for each method
 ├── logs/          # Pipeline execution logs
-├── metasigs/      # Generated meta-signatures
+├── signatures/      # Generated signatures
+├── overlap/      # overlap score for each signature
 └── scores/        # Evaluation scores and metrics
+
+# For -s integration.smk
+results/your_analysis/
+├── benchmarks/     # Performance benchmarks for each pipeline step
+├── data/           # Processed data files
+├── integration/    # Integrated datasets for each method
+├── logs/          # Pipeline execution logs
+├── eval/      # scib metrics for the latent spaces
+└── plotting/        # Umaps of the latent representations
 ```
 Each directory contains the intermediate and final results for that stage of the pipeline.
 

docs/source/tutorials/reproducing.md

@@ -29,7 +29,7 @@ python ccafetcher.py --metadata 3ca_test.csv --download-dir data/downloads --dat
 The signature analysis pipeline evaluates different gene signature methods across cancer datasets:
 
 ```bash
-snakemake --configfile config/signatures/<config>.yaml --sdm apptainer --apptainer-args "\\-\\-nvccli" -c <number_of_cores> -s signatures.smk
+snakemake --configfile configs/signatures/<config>.yaml --sdm apptainer --apptainer-args "\\-\\-nvccli" -c <number_of_cores> -s signatures.smk
 ```
 
 Available signature configuration files can be found at `configs/signatures`.
@@ -39,7 +39,7 @@ Available signature configuration files can be found at `configs/signatures`.
 The integration analysis pipeline benchmarks batch integration methods:
 
 ```bash
-snakemake --configfile config/integration/<config>.yaml --sdm apptainer --apptainer-args "\\-\\-nvccli" -c <number_of_cores> -s integration.smk
+snakemake --configfile configs/integration/<config>.yaml --sdm apptainer --apptainer-args "\\-\\-nvccli" -c <number_of_cores> -s integration.smk
 ```
 
 Available signature configuration files can be found at `configs/integration`.