add RNASeq.config

src/RNASeq.config

+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'
+      }
+    }
+  }
+}

src/RNASeq.nf

@@ -16,9 +16,9 @@ process adaptor_removal {
   set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
 
   script:
-  """
-  cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
-  -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
-  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+    """
+    cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+    -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+    ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
   """
 }