From 3da0a73c6da6d377450590e2326ac4c1dd7142e2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 3 May 2019 14:36:40 +0200
Subject: [PATCH] kallisto: indexing config sh conda env instead of source
---
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 a7604015..b51369e1 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -50,7 +50,7 @@ profiles {
ccin2p3_conda {
process{
withName: index_fasta {
- beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
--
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