From ed67f90c878a51dfaeb36f5304b3459072bfdc7b Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Mon, 30 Jul 2018 13:13:02 +0200
Subject: [PATCH] add fastqc and multiqc to config

---
 src/RNAseq_sen1D.config | 116 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 116 insertions(+)

diff --git a/src/RNAseq_sen1D.config b/src/RNAseq_sen1D.config
index d02f959..c47b0e0 100644
--- a/src/RNAseq_sen1D.config
+++ b/src/RNAseq_sen1D.config
@@ -1,3 +1,81 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $fastqc_fastq {
+        container = "fastqc:0.11.5"
+      }
+    }
+  }
+  sge {
+    process{
+      $fastqc_fastq {
+        beforeScript = "module purge; module load FastQC/0.11.5"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
+
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $fastqc_fastq_cutadapt {
+        container = "fastqc:0.11.5"
+      }
+    }
+  }
+  sge {
+    process{
+      $fastqc_fastq_cutadapt {
+        beforeScript = "module purge; module load FastQC/0.11.5"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
+
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $fastqc_fastq_randombp {
+        container = "fastqc:0.11.5"
+      }
+    }
+  }
+  sge {
+    process{
+      $fastqc_fastq_randombp {
+        beforeScript = "module purge; module load FastQC/0.11.5"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
+
 profiles {
   docker {
     docker.temp = 'auto'
@@ -131,3 +209,41 @@ profiles {
     }
   }
 }
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $fastqc_fastq {
+        container = "fastqc:0.11.5"
+      }
+      $multiqc {
+        container = "multiqc:1.0"
+      }
+    }
+  }
+  sge {
+    process{
+      $fastqc_fastq {
+        beforeScript = "module purge; module load FastQC/0.11.5"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+      $multiqc {
+        beforeScript = "module purge; module load FastQC/1.0"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
-- 
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