docs: use readme for index

CCBR · Sep 12, 2024 · 0b61d35 · 0b61d35
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diff --git a/README.md b/README.md
@@ -12,6 +12,6 @@
 
 This snakemake pipeline is built to run on [Biowulf](https://hpc.nih.gov/).
 
-For comments/suggestions/advice please reach out to [Samantha Chill](mailto:samantha.sevilla@nih.gov).
+For comments/suggestions/advice please contact <mailto:CCBR_Pipeliner@mail.nih.gov>.
 
-For detailed documentation on running the pipeline view the [documentation](https://CCBR.github.io/CARLISLE/) page.
+For detailed documentation on running the pipeline view the [documentation](https://CCBR.github.io/CARLISLE/) website.
diff --git a/resources/img/CUTandRUN_Workflow.jpeg → docs/img/CUTandRUN_Workflow.jpeg b/resources/img/CUTandRUN_Workflow.jpeg → docs/img/CUTandRUN_Workflow.jpeg
diff --git a/docs/index.md b/docs/index.md
@@ -1,3 +1,9 @@
+<!-- the README is inserted here automatically-->
+
+--8<-- "README.md"
+
+<!--- write additional info that you only want to appear in the docs index here -->
+
 The CARLISLE pipeline was developed in support of NIH [Dr Vassiliki Saloura's Laboratory](https://ccr.cancer.gov/staff-directory/vassiliki-saloura) and [Dr Javed Khan's Laboratory](https://ccr.cancer.gov/staff-directory/javed-khan/lab). It has been developed and tested solely on NIH [HPC Biowulf](https://hpc.nih.gov/).
 
-![Image title](https://github.com/CCBR/CARLISLE/blob/dev/resources/img/CUTandRUN_Workflow.jpeg?raw=true)
+![cut-and-run workflow](img/CUTandRUN_Workflow.jpeg)
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -91,7 +91,7 @@ markdown_extensions:
 
 # Page Tree
 nav:
-  - Background: index.md
+  - Home: index.md
   - Usage:
       - 1. Getting Started: user-guide/getting-started.md
       - 2. Preparing Files: user-guide/preparing-files.md