Merge pull request #1021 from nf-core/docker-registry-config-move

Set a default docker registry outside of profile scope.

Author: drpatelh

nextflow.config

@@ -168,7 +168,6 @@ profiles {
     }
     docker {
         docker.enabled         = true
-        docker.registry        = 'quay.io'
         docker.userEmulation   = true
         conda.enabled          = false
         singularity.enabled    = false
@@ -192,7 +191,6 @@ profiles {
     }
     podman {
         podman.enabled         = true
-        podman.registry        = 'quay.io'
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -263,6 +261,15 @@ 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
+docker.registry = 'quay.io'
+podman.registry = 'quay.io'
+
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true