From e636850aef932fc70321f802be83856dff57ee38 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Apr 2019 16:45:49 +0200
Subject: [PATCH] kallisto: config for in2p3, add /usr/bin to path
---
src/nf_modules/kallisto/indexing.config | 4 ++--
src/nf_modules/kallisto/indexing.nf | 2 --
2 files changed, 2 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 0dd7e42d..35dffe67 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withName: index_fasta {
+ withNamek index_fasta {
container = "kallisto:0.44.0"
cpus = 4
}
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:$PATH"
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/indexing.nf b/src/nf_modules/kallisto/indexing.nf
index 76b168b2..ea153569 100644
--- a/src/nf_modules/kallisto/indexing.nf
+++ b/src/nf_modules/kallisto/indexing.nf
@@ -10,7 +10,6 @@ Channel
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
- echo true
input:
file fasta from fasta_file
@@ -21,7 +20,6 @@ process index_fasta {
script:
"""
-pwd
kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
2> ${fasta.baseName}_kallisto_report.txt
"""
--
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