From 7e777c6626064d7463ecbf91c2c599db85eec647 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 24 May 2022 12:25:31 +0200
Subject: [PATCH] add error is  is provided twice

---
 modules/mosdepth/main.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf
index 1f503c6b..a5218286 100644
--- a/modules/mosdepth/main.nf
+++ b/modules/mosdepth/main.nf
@@ -31,6 +31,9 @@ process MOSDEPTH {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--fasta ${fasta}" : ""
     def interval = bed ? "--by ${bed}" : ""
+    if (bed && ext.args.contains("--by")) {
+        exit 1, "--by can only be specified once."
+    }
 
     """
     mosdepth \\