Update nextflow.config

restore process.shell declaration
nf-core · May 11, 2023 · deffccb · deffccb
1 parent 969be28
commit deffccb
Showing 1 changed file with 3 additions and 0 deletions.
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