From d31761217c48a253e4c905fa8903a17d83fe24da Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 20 Jan 2021 17:01:38 +0100
Subject: [PATCH] nextflow.config: add generic config file for module use
---
src/nextflow.config | 93 +++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 93 insertions(+)
create mode 100644 src/nextflow.config
diff --git a/src/nextflow.config b/src/nextflow.config
new file mode 100644
index 00000000..9239f5bd
--- /dev/null
+++ b/src/nextflow.config
@@ -0,0 +1,93 @@
+nextflowVersion = '>=25'
+
+manifest {
+ homePage = 'https://gitbio.ens-lyon.fr/LBMC/nextflow'
+ description = 'pipeline to '
+ mainScript = 'main.nf'
+ version = '0.0.0'
+}
+
+report {
+ enabled = true
+ file = "$baseDir/../results/report.html"
+}
+
+profiles {
+ docker {
+ docker.temp = "auto"
+ docker.enabled = true
+ process {
+ withLabel: big_mem_mono_cpus {
+ cpus = 1
+ }
+ withLabel: big_mem_multi_cpus {
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ singularity.cacheDir = "./bin/"
+ process {
+ withLabel: big_mem_mono_cpus {
+ cpus = 1
+ }
+ withLabel: big_mem_multi_cpus {
+ cpus = 4
+ }
+ }
+ }
+ psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "$baseDir/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
+ process{
+ withLabel: big_mem_mono_cpus {
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = "monointeldeb128"
+ }
+ withLabel: big_mem_multi_cpus {
+ scratch = true
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
+
+ }
+ }
+ }
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.cacheDir = "$baseDir/.singularity_in2p3/"
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withLabel: big_mem_mono_cpus {
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = "huge"
+ }
+ withLabel: big_mem_multi_cpus {
+ container = "lbmc/urqt:d62c1f8"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = "huge"
+ }
+ }
+ }
+}
--
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