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diff --git a/docs/index.md b/docs/index.md
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 The scrnaseq workflow comes with a good amount of documentation, found in the `docs/` directory:
 
-[Installation](docs/installation.md)   
-[Running the workflow](docs/usage_workflow.md)   
-[Running the pre-workflow](docs/usage_preworkflow.md)   
+[Installation](installation.md)   
+[Running the workflow](../misc/usage_workflow.md)   
 
 # Credits
 

diff --git a/docs/R_style_guide.txt → misc/R_style_guide.txt b/docs/R_style_guide.txt → misc/R_style_guide.txt
diff --git a/css/style.css → misc/style.css b/css/style.css → misc/style.css
diff --git a/docs/usage_preworkflow.md → misc/usage_preworkflow.md b/docs/usage_preworkflow.md → misc/usage_preworkflow.md
diff --git a/docs/usage_workflow.md → misc/usage_workflow.md b/docs/usage_workflow.md → misc/usage_workflow.md