refactor: include advanced execution

docs/installation.md

@@ -139,11 +139,15 @@ Given that the workflow has been properly deployed and configured, run Snakemake
 Snakemake will automatically detect the main Snakefile in the workflow subfolder
  and execute the workflow module that has been defined by the deployment.
 
-This workflow is written with Snakemake and details and tools are described in the
-[Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog?usage=IKIM-Essen/uncovar).
+If the user is only interested in getting a specific result, every intermediate
+ file of the analysis can be generated with including it in the execution
+ prompt, e.g. the FDR-controlled variant callings with major impact:
 
-If you use this workflow in your work, don't forget to give credits to the
-authors by citing the URL of this repository and its DOI (see above).
+```sh
+    snakemake --cores all --use-conda results/{date}/filtered-calls/ref~main/{sample}.subclonal-major.nofilter.orf.bcf
+```
+
+exchanging `date` and `sample` accordingly.
 
 ----------------
 ## General settings
@@ -159,3 +163,9 @@ The incoming directory should contain paired end reads in (compressed) FASTQ
 format. UnCoVar automatically copies your data into the data directory and moves
 all files from incoming directory to the archive. After the analysis, all results
 are compressed and saved alongside the reads.
+
+This workflow is written with Snakemake. Details are described in the
+[Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog?usage=IKIM-Essen/uncovar).
+
+If you use this workflow in your work, don't forget to give credits to the
+authors by citing the URL of this repository and its DOI (see above).

mkdocs.yml

@@ -8,7 +8,7 @@ repo_name: ""
 
 nav:
   - Overview: index.md
-  - Installation: installation.md
+  - Installation + Execution: installation.md
   - The Report: user-guide.md
   - Advanced Configuration: configuration.md
   - Tools: tools.md