Removed redundant function and updated documentation

docs/02-workflow/02-analysis.md

@@ -26,4 +26,37 @@ Reference Genome Configuration
 {:toc}
 </details>
 
----
+---
+
+<details>
+  <summary>Rule Map/Diagram</summary>
+
+  ```mermaid
+    flowchart TB
+      classDef bcftools stroke:#FF5733,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef plink stroke:#36454F,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef python stroke:#FEBE10,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef admixture stroke:#333,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef tabix stroke:#023020,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef gatk stroke:#007FFF,fill:#D3D3D3,stroke-width:4px,color:black;
+      START(((Input)))
+      END(((Output)))
+
+      extract_provided_region[[**extract_provided_region**: Extract the provided region coordinates for clustering]]
+
+      remove_rare_variants[[**remove_rare_variants**: Remove all variants which are not good indicators of population structure by nature]]
+
+      plinkPca[[**Plink_PCA**:
+  Perform a PLINK-2.0 PCA]]
+      
+      report_fixation_index_per_cluster[[**report_fixation_index_per_cluster**: Report Fixation-index for the provided clusters]]
+
+      class remove_rare_variants,plinkPca,plinkPed,report_fixation_index_per_cluster,extract_provided_region plink;
+      class Admixture admixture;
+      class fetchPedLables python;
+
+      START --> extract_provided_region --> remove_rare_variants --> plinkPca & report_fixation_index_per_cluster
+
+      plinkPca & report_fixation_index_per_cluster --> END
+  ```
+</details>

workflow/rules/common.smk

@@ -7,6 +7,3 @@ def outputDir(path: str) -> str:
         return join(OUTPUT_DIR_PATH, path)
     else:
         return join("results", path)
-
-def population_structure_outputs(wildcards):
-    return []