From 6f5fdc5b7f87df914e997d9c2cb6a76efad1db06 Mon Sep 17 00:00:00 2001
From: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Date: Sat, 18 May 2024 16:08:51 +0200
Subject: [PATCH 1/3] Update mkdocs.yml

---
 mkdocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mkdocs.yml b/mkdocs.yml
index 3467c546..119e770b 100644
--- a/mkdocs.yml
+++ b/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

From 4734eafaf0306960a75fa097f2c472dcfe7d04a1 Mon Sep 17 00:00:00 2001
From: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Date: Sat, 18 May 2024 16:21:16 +0200
Subject: [PATCH 2/3] add specific execution command example

---
 docs/installation.md | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/docs/installation.md b/docs/installation.md
index 43fc0647..51ce3f45 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -139,7 +139,17 @@ 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
+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:
+
+```sh
+    snakemake --cores all --use-conda results/{date}/filtered-calls/ref~main/{sample}.subclonal-major.nofilter.orf.bcf
+```
+
+exchanging `date` and `sample` accordingly.
+
+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

From 9d69487e2ef6c18f53a2ffcbcb513067a8b691aa Mon Sep 17 00:00:00 2001
From: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Date: Sat, 18 May 2024 16:22:18 +0200
Subject: [PATCH 3/3] move text

---
 docs/installation.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/installation.md b/docs/installation.md
index 51ce3f45..9b8f6e0b 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -149,12 +149,6 @@ If the user is only interested in getting a specific result, every intermediate
 
 exchanging `date` and `sample` accordingly.
 
-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).
-
 ----------------
 ## General settings
 
@@ -169,3 +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).