From a2a8e09762a5aec8985f0d93125eafe3a6d2d365 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 24 May 2022 13:45:52 +0200
Subject: [PATCH] Update modules/mosdepth/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/mosdepth/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf
index 39586797..5f6538e7 100644
--- a/modules/mosdepth/main.nf
+++ b/modules/mosdepth/main.nf
@@ -32,7 +32,7 @@ process MOSDEPTH {
     def reference = fasta ? "--fasta ${fasta}" : ""
     def interval = bed ? "--by ${bed}" : ""
     if (bed && args.contains("--by")) {
-        exit 1, "--by can only be specified once."
+        exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
     }
 
     """