From c8902c460309d3d8f986051aa26173fd7b297368 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Mar 2019 15:16:48 +0100
Subject: [PATCH] UrQt: switch cpus config from .nf to .config
---
src/nf_modules/UrQt/trimming_paired.config | 3 +++
src/nf_modules/UrQt/trimming_paired.nf | 1 -
src/nf_modules/UrQt/trimming_single.config | 3 +++
src/nf_modules/UrQt/trimming_single.nf | 2 +-
4 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/UrQt/trimming_paired.config b/src/nf_modules/UrQt/trimming_paired.config
index dd40a8b..de46593 100644
--- a/src/nf_modules/UrQt/trimming_paired.config
+++ b/src/nf_modules/UrQt/trimming_paired.config
@@ -4,6 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
+ cpus = 4
container = "urqt:d62c1f8"
}
}
@@ -12,6 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: trimming {
+ cpus = 4
container = "file:///bin/UrQt:d62c1f8.sif"
}
}
@@ -24,6 +26,7 @@ profiles {
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "5GB"
+ cpus = 16
time = "12h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
diff --git a/src/nf_modules/UrQt/trimming_paired.nf b/src/nf_modules/UrQt/trimming_paired.nf
index 7720b12..f15efac 100644
--- a/src/nf_modules/UrQt/trimming_paired.nf
+++ b/src/nf_modules/UrQt/trimming_paired.nf
@@ -7,7 +7,6 @@ Channel
process trimming {
tag "${reads}"
- cpus 4
publishDir "results/fastq/trimming/", mode: 'copy'
input:
diff --git a/src/nf_modules/UrQt/trimming_single.config b/src/nf_modules/UrQt/trimming_single.config
index dd40a8b..0324bb8 100644
--- a/src/nf_modules/UrQt/trimming_single.config
+++ b/src/nf_modules/UrQt/trimming_single.config
@@ -5,6 +5,7 @@ profiles {
process {
withName: trimming {
container = "urqt:d62c1f8"
+ cpus = 4
}
}
}
@@ -13,6 +14,7 @@ profiles {
process {
withName: trimming {
container = "file:///bin/UrQt:d62c1f8.sif"
+ cpus = 4
}
}
}
@@ -23,6 +25,7 @@ profiles {
module = "UrQt/d62c1f8"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 16
memory = "5GB"
time = "12h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/UrQt/trimming_single.nf b/src/nf_modules/UrQt/trimming_single.nf
index 5eb1e84..4116a69 100644
--- a/src/nf_modules/UrQt/trimming_single.nf
+++ b/src/nf_modules/UrQt/trimming_single.nf
@@ -10,7 +10,7 @@ Channel
process trimming {
tag "$file_id"
- cpus 4
+ echo true
input:
set file_id, file(reads) from fastq_files
--
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