From 8b66dd7322ddd59fb8354a1963e5d85adb06d080 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 16:50:38 +0200
Subject: [PATCH] SRAtoolkit: nf update psmn config
---
src/nf_modules/SRAtoolkit/fastqdump.config | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/SRAtoolkit/fastqdump.config b/src/nf_modules/SRAtoolkit/fastqdump.config
index d0e82733..bedbcd57 100644
--- a/src/nf_modules/SRAtoolkit/fastqdump.config
+++ b/src/nf_modules/SRAtoolkit/fastqdump.config
@@ -11,13 +11,12 @@ profiles {
psmn {
process{
withname: fastq_dump {
- beforeScript = "module purge; module load SRAtoolkit/2.8.2"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SRAtoolkit/2.8.2"
executor = "sge"
cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
+ memory = "20GB"
+ time = "12h"
queue = 'monointeldeb128'
}
}
--
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