docs: update workflow graph images (#40)

* docs: use SVG files to illustrate workflow graphs

* docs: rotate snakemake graphs

* docs: use details tag for rule graph images

Author: ahmig

.dag.png

@@ -207,26 +207,41 @@ All of the following variables are pre-defined in [config.yaml](/config/config.y
 Snakemake enables easy visualization of workflows and rule relationships. The `--rulegraph` option outputs a DOT file that describes dependencies between rules. The example below produces an image using Graphviz:
 
 ```shell
-snakemake --forceall --rulegraph | dot -Tpng >.rulegraph.png
+snakemake --forceall --rulegraph | dot -Grankdir=LR -Tsvg >.rulegraph.svg
 ```
 
-![Snakemake rule graph](/.rulegraph.png)
+<details>
+<summary>Rule graph image</summary>
+
+![Snakemake rule graph](/.rulegraph.svg)
+
+</details>
 
 The same graph can also be rendered with other tools such as [snakevision](https://github.com/OpenOmics/snakevision) (v0.1.0).
 
 ```shell
 snakemake --forceall --rulegraph | snakevision -s all -o .rulegraph_sv.svg
 ```
 
+<details>
+<summary>Snakevision rule graph image</summary>
+
 ![Snakemake rule graph using snakevision](/.rulegraph_sv.svg)
 
-The `--dag` option emits an directed acyclic graph (DAG) that corresponds to the rule instances that would be executed for the current dataset. The example below produces an image using Graphviz:
+</details>
+
+The `--dag` option emits an directed acyclic graph (DAG) that corresponds to the rule instances that would be executed for the target dataset. The example below produces an image using Graphviz (for [data](https://doi.org/10.20350/digitalCSIC/15648) from [our study](https://doi.org/10.1093/ve/veae018)):
 
 ```shell
-snakemake --forceall --dag | dot -Tpng >.dag.png
+snakemake --forceall --dag | dot -Grankdir=LR -Tsvg >.dag.svg
 ```
 
-![Snakemake DAG](/.dag.png)
+<details>
+<summary>DAG image</summary>
+
+![Snakemake DAG](/.dag.svg)
+
+</details>
 
 ## Run modes