From 299253e7b334996dded443c563be50cd694df2ed Mon Sep 17 00:00:00 2001
From: z483800 <109-z483800@users.noreply.gitlab.biologie.ens-lyon.fr>
Date: Fri, 17 Jan 2020 14:30:41 +0000
Subject: [PATCH] Update src/RNAseq.config

---
 src/RNAseq.config | 53 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 src/RNAseq.config

diff --git a/src/RNAseq.config b/src/RNAseq.config
new file mode 100644
index 0000000..ed42799
--- /dev/null
+++ b/src/RNAseq.config
@@ -0,0 +1,53 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: adaptor_removal {
+        container = "lbmc/cutadapt:2.4"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    singularity.cacheDir = "./bin/"
+    process {
+      withName: adaptor_removal {
+        container = "lbmc/cutadapt:2.4"
+        cpus = 1
+      }
+    }
+  }
+  psmn{
+    process{
+      withName: adaptor_removal {
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.4"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+      }
+    }
+  }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.cacheDir = "$baseDir/.singularity_in2p3/"
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: adaptor_removal {
+        container = "lbmc/cutadapt:2.4"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
+}
-- 
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