new pipeline_bowtie2_nosplit bam

src/RNAseq_sen1D_bowtie2_nosplit.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $fastqc_fastq {
+        container = "fastqc:0.11.5"
+      }
+      $fastqc_fastq_cutadapt {
+        container = "fastqc:0.11.5"
+      }
+      $fastqc_fastq_randombp {
+        container = "fastqc:0.11.5"
+      }
+      $fastqc_fastq_urqt {
+        container = "fastqc:0.11.5"
+      }
+      $adaptor_removal {
+      container = "cutadapt:1.14"
+      }
+      $multiqc {
+        container = "multiqc:1.0"
+      }
+      $random_bases_4_trimming {
+        container = "cutadapt:1.14"
+      }
+      $trimming {
+        container = "urqt:d62c1f8"
+      }
+      $index_fasta {
+        container = "bowtie2:2.3.4.1"
+      }
+      $mapping_fastq {
+        container = "bowtie2:2.3.4.1"
+      }
+      $sort_bam {
+        container = "samtools:1.7"
+      }
+      $index_bam {
+        container = "samtools:1.7"
+      }
+    }
+  }
+  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'
+      }
+      $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'
+      }
+      $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'
+      }
+      $fastqc_fastq_urqt {
+        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'
+      }
+      $adaptor_removal {
+        beforeScript = "module purge; module load cutadapt/1.14"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
+      }
+      $random_bases_4_trimming {
+        beforeScript = "module purge; module load cutadapt/1.14"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
+      }
+      $trimming {
+        beforeScript = "module purge; module load UrQt/d62c1f8"
+        executor = "sge"
+        cpus = 4
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
+      }
+      $index_fasta {
+        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+      }
+      $mapping_fastq {
+        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+      }
+      $sort_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+      $index_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+    }
+  }
+}