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Verified Commit 09e2b2fc authored by Laurent Modolo's avatar Laurent Modolo
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in2p3 test: make singularity default for ccin2p3

parent 883c3c3e
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......@@ -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}"
......@@ -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'
}
......
......@@ -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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