From e16a1a9ff401e18491a989e95660f4ecf2003e6d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 11:18:35 +0200
Subject: [PATCH] kallisto: add in2p3 config
---
src/nf_modules/kallisto/indexing.config | 6 ++----
src/nf_modules/kallisto/mapping_paired.config | 15 +++++++++++++++
src/nf_modules/kallisto/mapping_single.config | 15 +++++++++++++++
3 files changed, 32 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 403d9426..84c2a2f4 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -42,11 +42,9 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 4
- memory = "8GB"
+ cpus = 1
+ memory = "10GB"
time = "24h"
- queue = 'mc_huge'
- penv = 'multicores'
}
}
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index a8c439b9..48ee3405 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -33,6 +33,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: mapping_fastq {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index a8c439b9..48ee3405 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -33,6 +33,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: mapping_fastq {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
--
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