From 09e2b2fc325b7083c12ddea573f18167d6dd647b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 20 May 2019 16:07:44 +0200
Subject: [PATCH] in2p3 test: make singularity default for ccin2p3
---
src/kallisto_index.pbs | 4 ++--
src/nf_modules/kallisto/indexing.config | 7 +++----
src/nf_modules/kallisto/indexing.nf | 3 ---
3 files changed, 5 insertions(+), 9 deletions(-)
diff --git a/src/kallisto_index.pbs b/src/kallisto_index.pbs
index 257b301f..c34affd3 100644
--- a/src/kallisto_index.pbs
+++ b/src/kallisto_index.pbs
@@ -24,6 +24,6 @@ PIPELINE=${SCRATCH}/nextflow/src/nf_modules/kallisto/indexing.nf
# change to your project / pipeline !
CONFIG=${SCRATCH}/nextflow/src/nf_modules/kallisto/indexing.config
-${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3_singularity \
+${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
--fasta "${SCRATCH}/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta" \
--w "${SCRATCH}" -ansi-log false
+-w "${SCRATCH}"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 752c099b..84722f6d 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -33,7 +33,7 @@ profiles {
}
}
}
- ccin2p3 {
+ ccin2p3_conda {
process{
withName: index_fasta {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
@@ -49,19 +49,18 @@ profiles {
}
}
}
- ccin2p3_singularity {
+ ccin2p3 {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- beforeScript = "export SINGULARITY_BIND=\"/sps,/scratch:/var/singularity/mnt/\""
container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o /sps/lbmc/lmodolo/logs/ -e /sps/lbmc/lmodolo/logs/ -M laurent.modolo@ens-lyon.fr -m beas"
+ -o ~/logs/ -e ~/logs/"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/kallisto/indexing.nf b/src/nf_modules/kallisto/indexing.nf
index f24b0c1c..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
@@ -21,10 +20,8 @@ process index_fasta {
script:
"""
-pwd
kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
2> ${fasta.baseName}_kallisto_report.txt
-pwd
"""
}
--
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