From f6921da8350eaedf4943b1aa95f21ca1ead6252e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 20 May 2019 15:03:23 +0200
Subject: [PATCH] in2p3 test: fix beforeScript config
---
src/nf_modules/kallisto/indexing.config | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index e0fef67a..35a01e62 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.autoMounts = true
process{
withName: index_fasta {
- beforeScript = "export SINGULARITY_BIND="/sps,/scratch:/var/singularity/mnt/""
+ beforeScript = "export SINGULARITY_BIND=\"/sps,/scratch:/var/singularity/mnt/\""
container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
scratch = true
stageInMode = "copy"
--
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