From 47f161fd17095cb1c92c27b68376a3701c2a8942 Mon Sep 17 00:00:00 2001
From: Olga Botvinnik <olga.botvinnik@gmail.com>
Date: Mon, 24 Jun 2019 17:30:39 -0700
Subject: [PATCH] Add docker.runOptions to avoid memory swap error

---
 .../{{cookiecutter.name_noslash}}/nextflow.config            | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
index 6f0d53a0bb..f684adc20f 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -58,6 +58,11 @@ profiles {
   test { includeConfig 'conf/test.config' }
 }
 
+// Avoid this error:
+// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
+// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker
+docker.runOptions = '-u $(id -u):$(id -g)'
+
 // Load igenomes.config if required
 if(!params.igenomesIgnore){
   includeConfig 'conf/igenomes.config'