corrections fichier config fastqc

src/RNAseq_sen1D.config

@@ -6,6 +6,48 @@ profiles {
       $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_forward {
+        container = "samtools:1.7"
+      }
+      $index_bam_forward {
+        container = "samtools:1.7"
+      }
+      $sort_bam_reverse {
+        container = "samtools:1.7"
+      }
+      $index_bam_reverse {
+        container = "samtools:1.7"
+      }
+      $split_bam {
+        container = "samtools:1.7"
+      }
     }
   }
   sge {
@@ -20,22 +62,6 @@ profiles {
         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"
@@ -46,23 +72,17 @@ profiles {
         pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
-    }
-  }
-}
-
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
       $fastqc_fastq_randombp {
-        container = "fastqc:0.11.5"
+        beforeScript = "module purge; module load FastQC/0.11.5"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
       }
-    }
-  }
-  sge {
-    process{
-      $fastqc_fastq_randombp {
+      $fastqc_fastq_urqt {
         beforeScript = "module purge; module load FastQC/0.11.5"
         executor = "sge"
         cpus = 1
@@ -72,25 +92,16 @@ profiles {
         pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
-    }
-  }
-}
-
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-    $adaptor_removal {
-      container = "cutadapt:1.14"
-    }
-    $random_bases_4_trimming {
-      container = "cutadapt:1.14"
-    }
-    }
-  }
-  sge {
-    process{
+      $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"
@@ -102,7 +113,6 @@ profiles {
         queue = 'h6-E5-2667v4deb128'
         penv = 'openmp8'
       }
-
       $random_bases_4_trimming {
         beforeScript = "module purge; module load cutadapt/1.14"
         executor = "sge"
@@ -114,21 +124,6 @@ profiles {
         queue = 'h6-E5-2667v4deb128'
         penv = 'openmp8'
       }
-    }
-  }
-}
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $trimming {
-        container = "urqt:d62c1f8"
-      }
-    }
-  }
-  sge {
-    process{
       $trimming {
         beforeScript = "module purge; module load UrQt/d62c1f8"
         executor = "sge"
@@ -140,57 +135,12 @@ profiles {
         queue = 'h6-E5-2667v4deb128'
         penv = 'openmp8'
       }
-    }
-  }
-}
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "bowtie2:2.3.4.1"
-      }
-      $mapping_fastq {
-        container = "bowtie2:2.3.4.1"
-      }
-    }
-  }
-  sge {
-    process{
       $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"
       }
-    }
-  }
-}
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $sort_bam_forward {
-        container = "samtools:1.7"
-      }
-      $index_bam_forward {
-        container = "samtools:1.7"
-      }
-      $sort_bam_reverse {
-        container = "samtools:1.7"
-      }
-      $index_bam_reverse {
-        container = "samtools:1.7"
-      }
-      $split_bam {
-        container = "samtools:1.7"
-      }
-    }
-  }
-  sge {
-    process{
       $sort_bam_forward {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
@@ -209,41 +159,3 @@ 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'
-      }
-    }
-  }
-}