From bf418ede64ada407d14a9a9d0c5c813df69d465d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 May 2019 17:17:56 +0200
Subject: [PATCH] nextflow: update in2p3 test for demon queue
---
src/nextflow.pbs | 4 ++--
src/nf_modules/kallisto/indexing.config | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nextflow.pbs b/src/nextflow.pbs
index 68981b60..8f33cf9d 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 43e3ced0..a9e74c20 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"
--
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