Update nextflow.config

maxulysse · web-flow · commit deffccbeacad · 2023-05-11T11:15:51.000+02:00
restore process.shell declaration
diff --git a/nextflow.config b/nextflow.config
@@ -261,6 +261,9 @@ env {
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
 }
 
+// Capture exit codes from upstream processes when piping
+process.shell = ['/bin/bash', '-euo', 'pipefail']
+
 // Set default registry for Docker and Podman independent of -profile
 // Will not be used unless Docker / Podman are enabled
 // Set to your registry if you have a mirror of containers

Original file line number	Diff line number	Diff line change
`@@ -261,6 +261,9 @@ env {`
`261`	`261`	`JULIA_DEPOT_PATH = "/usr/local/share/julia"`
`262`	`262`	`}`
`263`	`263`
	`264`	`+// Capture exit codes from upstream processes when piping`
	`265`	`+process.shell = ['/bin/bash', '-euo', 'pipefail']`
	`266`	`+`
`264`	`267`	`// Set default registry for Docker and Podman independent of -profile`
`265`	`268`	`// Will not be used unless Docker / Podman are enabled`
`266`	`269`	`// Set to your registry if you have a mirror of containers`