SNP_calling.nf: add SGE config

src/SNP_calling.config

@@ -53,48 +53,136 @@ profiles {
         beforeScript = "module purge; module load cutadapt/1.14"
         executor = "sge"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
+        memory = "20GB"
+        time = "12h"
         queueSize = 1000
         pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        queue = 'monointeldeb128'
       }
       withName: trimming {
         beforeScript = "module purge; module load UrQt/d62c1f8"
         executor = "sge"
-        cpus = 4
+        cpus = 16
         memory = "5GB"
-        time = "6h"
+        time = "12h"
         queueSize = 1000
         pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
       withName: index_fasta {
-        beforeScript = "module purge; module load BWA/0.7.17"
+        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
         executor = "sge"
         cpus = 1
-        memory = "5GB"
+        memory = "30GB"
         time = "6h"
         queueSize = 1000
         pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        queue = 'monointeldeb128'
       }
       withName: mapping_fastq {
-        beforeScript = "module purge; module load BWA/0.7.17"
+        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
         executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
+        cpus = 16
+        memory = "30GB"
+        time = "12h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: merge_bam {
+        beforeScript = "module purge; module load sambamba/0.6.7"
+        executor = "sge"
+        cpus = 16
+        memory = "30GB"
+        time = "12h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: sort_bam {
+        beforeScript = "module purge; module load sambamba/0.6.7"
+        executor = "sge"
+        cpus = 16
+        memory = "30GB"
+        time = "12h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: index_bam {
+        beforeScript = "module purge; module load sambamba/0.6.7"
+        executor = "sge"
+        cpus = 16
+        memory = "30GB"
+        time = "12h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: index2_fasta {
+        beforeScript = "module purge; module load gatk/4.0.8.1"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+      withName: index3_fasta {
+        beforeScript = "module purge; module load SAMtools/1.7"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+      withName: samtools_SNP_tumor {
+        beforeScript = "module purge; module load bcftools/1.7"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+      withName: samtools_SNP_norm {
+        beforeScript = "module purge; module load bcftools/1.7"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
+      }
+      withName: vcf_to_csv_tumor {
+        beforeScript = "module purge; module load gatk/4.0.8.1"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
         queueSize = 1000
         pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        queue = 'monointeldeb128'
       }
-      withName: dedup_sam {
-        beforeScript = "module purge; module load samblaster/0.1.24"
+      withName: vcf_to_csv_norm {
+        beforeScript = "module purge; module load gatk/4.0.8.1"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'monointeldeb128'
       }
     }
   }