From cc561f9afd0c2873ffb9e68de74809349e63b429 Mon Sep 17 00:00:00 2001
From: Louisa Perelo <louisa.perelo@qbic.uni-tuebingen.de>
Date: Thu, 6 Apr 2023 16:59:17 +0200
Subject: [PATCH] update README

---
 README.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/README.md b/README.md
index 382184b..36aa1e9 100644
--- a/README.md
+++ b/README.md
@@ -23,8 +23,21 @@ See [here](https://nf-co.re/docs/usage/installation) how to install `nextflow` o
 
 ## Usage
 ### Re-run this ARCs analysis
+If you would like to re-run the workflow inside this ARC, you can do this via the `cwltool` as follows:
+```bash
+   cwltool ./workflows/nfcore_funcscan.cwl ./runs/nfcore_funcscan_yam.yml
+   ```
+
+If you prefer to use `nextflow` directly, navigate into the `runs`-folder and call
+```bash
+    sh funcscan_yam.sh
+    ````
 
 ### Apply the workflow to your own data
+If you would like to run `nf-core/funcscan` on your own data, generate a [samplesheet](https://nf-co.re/funcscan/1.0.1/usage#samplesheet-input) specifying the paths to your data-files. Then, create your own `.yml` file setting the `input:`-parameter to your `samplesheet.csv`. Specify any parameter changes in your `.yml` file.
+
+Alternatively, you can modify the `.sh` file by setting the `--input` parameter to your `samplesheet.csv`.
+
 
 ## Support
 Please contact DataPlant's [Helpdesk](https://helpdesk.nfdi4plants.org) for questions and support.
-- 
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