From ebecfb6dc6ec771e44b543e541e426edd3625cf7 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 27 Jan 2021 14:39:32 +0100
Subject: [PATCH] nextflow.config: add memory limits
---
src/nextflow.config | 11 +++++++----
src/nf_modules/picard/main.nf | 1 -
2 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/src/nextflow.config b/src/nextflow.config
index dfebf4d3..df01d720 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -17,6 +17,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
+ memory = '16 GB'
withLabel: big_mem_mono_cpus {
cpus = 1
}
@@ -29,6 +30,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
+ memory = '16 GB'
withLabel: big_mem_mono_cpus {
cpus = 1
}
@@ -46,7 +48,7 @@ profiles {
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
- memory = "20GB"
+ memory = "128GB"
time = "12h"
queue = "monointeldeb128"
}
@@ -55,7 +57,7 @@ profiles {
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
- memory = "30GB"
+ memory = "192GB"
time = "24h"
queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D"
penv = "openmp32"
@@ -75,6 +77,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
+ memory = "8GB"
queue = "huge"
}
withLabel: big_mem_multi_cpus {
@@ -83,9 +86,9 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
+ memory = "8GB"
queue = "huge"
}
}
diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf
index 9a6b702f..0faec2e0 100644
--- a/src/nf_modules/picard/main.nf
+++ b/src/nf_modules/picard/main.nf
@@ -6,7 +6,6 @@ process mark_duplicate {
label "big_mem_mono_cpus"
tag "$file_id"
publishDir "results/mapping/ddup/", mode: 'copy'
- memory '30 GB'
input:
tuple val(file_id), path(bam)
--
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