diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index a7604015cb79602725c793c89d1ae1440bdac176..b51369e15222c19f5ae02e8641d51d8fa18fc538 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"