diff --git a/.gitignore b/.gitignore
index bd1adf1f..84e3de44 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,10 +1,8 @@
 # Misc
-cytospace
-show_small.py
-archive/
 workflow/.snakemake
 workflow/logs
 *ignore*
+archive/
 explore
 sandbox
 
@@ -14,7 +12,7 @@ sandbox
 # Documentation
 site
 
-# Code Ocean related
+# Code Ocean
 code
 results
 
@@ -25,15 +23,6 @@ lightning_logs
 checkpoints
 run.log
 
-# Data files
-data/*/*
-!data/aml/default.csv
-!data/aml/short.h5ad
-!data/bmmc/default.csv
-!data/poised/default.csv
-!data/debarcoding/default.csv
-!data/README.md
-
 # Jupyter Notebook
 .ipynb_checkpoints
 exploration/*
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 2118ea84..0a70946e 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -8,9 +8,9 @@ Contributions are welcome as we aim to continue improving the pipeline. For inst
 - Submitting a fix
 - Proposing new features
 
-## Contributing to the code, or debugging
+## Pull Requests
 
-Even though *sopa* is meant for flamingo, you can set up this repository locally for development or debugging purposes.
+To add some new code to **sopa**, you should:
 
 1. Install the dependencies.
 2. Create your personal branch from `master`.
@@ -21,8 +21,7 @@ Even though *sopa* is meant for flamingo, you can set up this repository locally
 ## Coding guidelines
 
 - Use the `black` formatter and `isort`. Their usage should be automatic as they are in the `pyproject.toml` file. Depending on your IDE, you can choose to format your code on save.
-- Follow the [PEP8](https://peps.python.org/pep-0008/) style guide. In particular, use snake_case notations (and PascalCase for classes).
+- Follow the [PEP8](https://peps.python.org/pep-0008/) style guide.
 - Provide meaningful names to all your variables and functions.
 - Document your functions and type your function inputs/outputs.
-- Create your functions in the intended file, or create one if needed. See the project layout.
 - Try as much as possible to follow the same coding style as the rest of the repository.
\ No newline at end of file
diff --git a/workflow/_Snakefile b/workflow/_Snakefile
deleted file mode 100644
index ccf10840..00000000
--- a/workflow/_Snakefile
+++ /dev/null
@@ -1,68 +0,0 @@
-import utils
-
-### Required command line arguments
-
-# region: relative path to the region folder 
-# config: name of the config file to be used
-relative_region = config["region"]
-config_name = config["config"]
-
-run = utils.WorkflowPaths(relative_region, config_name)
-
-file = "..."
-sdata_path = f"{file}.zarr"
-config = "..."
-
-rule all:
-    input:
-        "..."
-
-checkpoint write_sdata:
-    input:
-        file,
-        config,
-    output:
-        sdata_path,
-        poly_paths_file,
-    shell:
-        f"""
-        python -m sopa.io.qptiff -p {file} -s {sdata_path} -c {config}
-        ... # write file with paths
-        """
-
-def get_input_patches(wilcards):
-    with open(checkpoints.write_sdata.get(**wilcards).output[1], 'r') as f:
-        n_tiles = int(json.load(f)["window_grid"]["num_tiles"])
-    return ...
-
-rule patch_segmentation:
-    input:
-        run.out.spec,
-    output:
-        f"{run.out.tiles_dir}/{{index}}.parquet",
-    resources:
-        mem_mb=3_000
-    conda:
-        "vpt"
-    shell:
-        f"""
-        vpt --verbose run-segmentation-on-tile \
-            --input-segmentation-parameters {run.out.spec} \
-            --tile-index {{wildcards.index}}
-        """
-
-rule aggregate_patches:
-    input:
-        run.out.spec,
-        get_input_patches,
-    output:
-        run.out.polygons,
-    resources:
-        mem_mb=32_000
-    conda:
-        "vpt"
-    shell:
-        f"""
-        vpt --verbose compile-tile-segmentation \
-            --input-segmentation-parameters {run.out.spec}
-        """
\ No newline at end of file