From 7a531d560ffee0581d0276d7554b1bb4a7b5d789 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 21 Jan 2025 16:11:51 +0100
Subject: [PATCH] Apply patch see here
 (https://github.com/nf-core/tools/pull/3416)

---
 nextflow.config | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 83c59a7..7589904 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -287,13 +287,13 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+]
 """
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.