From 03e156f89bfcd83ebbd053b371c1686aa461e232 Mon Sep 17 00:00:00 2001
From: Felix Lenner <52530259+fellen31@users.noreply.github.com>
Date: Wed, 25 Sep 2024 15:29:27 +0200
Subject: [PATCH] Revert back to using <TAG> for run example

---
 README.md | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 082288ba..5d1d9760 100644
--- a/README.md
+++ b/README.md
@@ -66,14 +66,15 @@ NIST,HG002,/path/to/HG002.fastq.gz,FAM1,HG003,HG004,1,2
 NIST,HG005,/path/to/HG005.bam,FAM1,HG003,HG004,2,1
 ```
 
-Supply a reference genome with `--fasta` and choose a matching `--preset` for your data (`revio`, `pacbio`, `ONT_R10`). Now, you can run the pipeline, e.g:
+Supply a reference genome with `--fasta` and choose a matching `--preset` for your data (`revio`, `pacbio`, `ONT_R10`). Now, you can run the pipeline using:
 
 ```bash
-nextflow run genomic-medicine-sweden/nallo -profile YOURPROFILE \
+nextflow run genomic-medicine-sweden/nallo \
+    -profile <docker/singularity/.../institute> \
     --input samplesheet.csv \
-    --preset revio \
-    --fasta  reference.fasta \
-    --outdir results
+    --preset <revio/pacbio/ONT_R10> \
+    --fasta <REFERENCE> \
+    --outdir <OUTDIR>
 ```
 
 For more details and further functionality, please refer to the [usage documentation](https://github.com/genomic-medicine-sweden/nallo/blob/dev/docs/usage.md).