From ff936828f96619a53afe258bc70a093243ae480e Mon Sep 17 00:00:00 2001
From: Julian Thomas Mohr <julian.mohr@tron-mainz.de>
Date: Wed, 26 Jul 2023 09:57:48 +0200
Subject: [PATCH] Enable Singularity containerization in nextflow.config

---
 nextflow.config | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index c31d793..bff7f39 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -46,14 +46,22 @@ profiles {
     }
     conda {
         conda.enabled = true
+        singularity.enabled = false
         params.enable_conda = true
         conda.createTimeout = "120 min"
     }
     mamba {
         conda.enabled = true
+        conda.useMamba = true
+        singularity.enabled = false
         params.enable_conda = true
         conda.createTimeout = "120 min"
-        conda.useMamba = true
+    }
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+        conda.enabled = false
+        params.enable_conda = false
     }
     test { 
         includeConfig 'conf/test.config' 
@@ -70,6 +78,11 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
+// Set default registry for Singularity independent of -profile
+// Will not be used unless Singularity is enabled
+// Set to your registry if you have a mirror of containers
+singularity.registry = 'quay.io'
+
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true