From e069611cfd7cdc07c1910bfa50ed8b7c1d35829b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 15:58:31 +0200
Subject: [PATCH] kallisto: add ccin2p3_conda profile for indexing
---
src/nf_modules/kallisto/indexing.config | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 84c2a2f4..86a36509 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -48,4 +48,20 @@ profiles {
}
}
}
+ ccin2p3_conda {
+ process{
+ withName: index_fasta {
+ beforeScript = "source /sps/lbmc/common/miniconda2/init.sh"
+ conda = "/sps/lbmc/common/miniconda2/envs/kallisto_0.44.0"
+ 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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