From e336cd2a506a218bd9ef48b0a5cf67a7feb599f4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 13:35:10 +0200
Subject: [PATCH] sratoolkit: add in2p3 config
---
src/nf_modules/sratoolkit/fastqdump.config | 15 +++++++++++++++
1 file changed, 15 insertions(+)
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 043a3784..8c1087e5 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -32,4 +32,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: fastq_dump {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sratoolkit/2.8.2/:/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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