SNP_calling.config: add bioawk for sge

src/SNP_calling.config

@@ -49,14 +49,14 @@ profiles {
   }
   sge {
     process{
+      queueSize = 1000
+      pollInterval = '60sec'
       withName: adaptor_removal {
         beforeScript = "module purge; module load cutadapt/1.14"
         executor = "sge"
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queueSize = 1000
-        pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
       withName: trimming {
@@ -65,19 +65,23 @@ profiles {
         cpus = 16
         memory = "5GB"
         time = "12h"
-        queueSize = 1000
-        pollInterval = '60sec'
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
         penv = 'openmp16'
       }
+      withName: filter_fasta {
+        beforeScript = "module purge; module load bioawk/1.0"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
       withName: index_fasta {
         beforeScript = "module purge; module load Bowtie2/2.3.4.1; module load sambamba/0.6.7; module load samblaster/0.6.7"
         executor = "sge"
         cpus = 1
         memory = "30GB"
         time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
       withName: mapping_fastq {
@@ -86,8 +90,6 @@ profiles {
         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'
       }
@@ -97,8 +99,6 @@ profiles {
         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'
       }
@@ -108,8 +108,6 @@ profiles {
         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'
       }
@@ -119,8 +117,6 @@ profiles {
         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'
       }
@@ -130,8 +126,6 @@ profiles {
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queueSize = 1000
-        pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
       withName: index3_fasta {
@@ -140,8 +134,6 @@ profiles {
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queueSize = 1000
-        pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
       withName: samtools_SNP_tumor {
@@ -150,8 +142,6 @@ profiles {
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queueSize = 1000
-        pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
       withName: samtools_SNP_norm {
@@ -160,8 +150,6 @@ profiles {
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queueSize = 1000
-        pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
       withName: vcf_to_csv_tumor {
@@ -170,8 +158,6 @@ profiles {
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queueSize = 1000
-        pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
       withName: vcf_to_csv_norm {
@@ -180,8 +166,6 @@ profiles {
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queueSize = 1000
-        pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
     }