diff --git a/src/nextflow.pbs b/src/nextflow.pbs
index 68981b60abc3050f45e664a85a38543d8cbdf493..8f33cf9d8ac339eb9bd086be38cc2314f432d69e 100644
--- a/src/nextflow.pbs
+++ b/src/nextflow.pbs
@@ -2,7 +2,6 @@
 #####################################
 # job script example with GE options
 #####################################
-#$ -S "/usr/local/bin/bash -l"
 #$ -q demon
 #$ -l demon=1
 #$ -P P_lbmc
@@ -16,11 +15,12 @@
 #$ -l sps=1   ## acces /sps directory
 #####################################
 
+NF=/pbs/throng/lbmc/cl7/nextflow/19.04/nextflow
 PIPELINE=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.nf
 CONFIG=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.config
 OPTIONx="--fasta \"data/tiny_dataset/fasta/tiny_v2.fasta\""
 
-time /pbs/throng/lbmc/cl7/nextflow/19.01/nextflow \
+time $NF \
 -profile ccin2p3_conda \
 $PIPELINE \
 -c $CONFIG \
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 43e3ced06bac6d2931249d8c6bc77bba42aa4fd6..a9e74c203c091e86728998b1f6fc15c3a1ad3031 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -50,8 +50,8 @@ profiles {
   ccin2p3_conda {
     process{
       withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda2/init.sh"
-        conda = "/sps/lbmc/common/miniconda2/envs/kallisto_0.44.0"
+        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
+        conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"