diff --git a/docs/02-workflow/02-analysis.md b/docs/02-workflow/02-analysis.md index fe756cb..62fab55 100644 --- a/docs/02-workflow/02-analysis.md +++ b/docs/02-workflow/02-analysis.md @@ -32,31 +32,32 @@ Reference Genome Configuration Rule Map/Diagram ```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))) +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]] + 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]] + remove_rare_variants[[**remove_rare_variants**: Remove all variants which are not good indicators of population structure by nature]] - plinkPca[[**Plink_PCA**: + 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]] + + 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; + 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 + START --> extract_provided_region --> remove_rare_variants --> plinkPca & report_fixation_index_per_cluster - plinkPca & report_fixation_index_per_cluster --> END + plinkPca & report_fixation_index_per_cluster --> END ``` + \ No newline at end of file