Strongly recommend snakemake

SchlossLab · Nov 30, 2022 · b4cf70e · b4cf70e
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diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,4 @@ inst/doc
 .snakemake
 /doc/
 /Meta/
+README.html
diff --git a/README.Rmd b/README.Rmd
@@ -1,7 +1,6 @@
 ---
 output:
-    github_document:
-      html_preview: false
+  github_document
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -97,10 +96,16 @@ You can watch the Riffomonas Project series of
 [video tutorials](https://www.youtube.com/playlist?list=PLmNrK_nkqBpKpzb9-vI4V7SdXC-jXEcmg) 
 covering mikropml and other skills related to machine learning.
 
-We also
-provide an [example Snakemake
-workflow](https://github.com/SchlossLab/mikropml-snakemake-workflow) for running
-`mikropml` on an HPC.
+We also provide a 
+[Snakemake workflow](https://github.com/SchlossLab/mikropml-snakemake-workflow) 
+for running `mikropml` locally or on an HPC.
+We highly recommend running `mikropml` with Snakemake or another workflow 
+management system for reproducibility and scalability of ML analyses.
+
+<a href="https://github.com/SchlossLab/mikropml-snakemake-workflow">
+<img src="https://raw.githubusercontent.com/SchlossLab/mikropml-snakemake-workflow/main/figures/mikropml-snakemake-workflow.png" 
+height="120" align="center" />
+</a>
 
 ## Help & Contributing
 

diff --git a/README.md b/README.md
@@ -72,9 +72,15 @@ You can watch the Riffomonas Project series of [video
 tutorials](https://www.youtube.com/playlist?list=PLmNrK_nkqBpKpzb9-vI4V7SdXC-jXEcmg)
 covering mikropml and other skills related to machine learning.
 
-We also provide an [example Snakemake
+We also provide a [Snakemake
 workflow](https://github.com/SchlossLab/mikropml-snakemake-workflow) for
-running `mikropml` on an HPC.
+running `mikropml` locally or on an HPC. We highly recommend running
+`mikropml` with Snakemake or another workflow management system for
+reproducibility and scalability of ML analyses.
+
+<a href="https://github.com/SchlossLab/mikropml-snakemake-workflow">
+<img src="https://raw.githubusercontent.com/SchlossLab/mikropml-snakemake-workflow/main/figures/mikropml-snakemake-workflow.png" 
+height="120" align="center" /> </a>
 
 ## Help & Contributing