add shell guards

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 = ""