From 37d2e6c7554b216c2734cbb8a03bd7f3f4cc70c5 Mon Sep 17 00:00:00 2001
From: Chris Wright <chris.wright@nanoporetech.com>
Date: Mon, 15 Feb 2021 15:22:13 +0000
Subject: [PATCH] add shell guards

---
 nextflow.config | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index 2c8eb72..02bcbb5 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -24,6 +24,7 @@ profiles {
             withLabel:pysam {
                 container = 'ontresearch/workflow-template:latest'
             }
+            shell = ['/bin/bash', '-euo', 'pipefail']
         }
     }
     
@@ -37,6 +38,7 @@ profiles {
             withLabel:pysam {
                 conda = "environment.yaml"
             }
+            shell = ['/bin/bash', '-euo', 'pipefail']
         }
         conda {
              cacheDir = ""