Skip to content
Snippets Groups Projects
Commit ea17baf9 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

SNP_calling.config: add bioawk for sge

parent ec7d1b21
No related branches found
No related tags found
1 merge request!10Module for BWA GATK sambamba samblaster and bcftools
...@@ -49,14 +49,14 @@ profiles { ...@@ -49,14 +49,14 @@ profiles {
} }
sge { sge {
process{ process{
queueSize = 1000
pollInterval = '60sec'
withName: adaptor_removal { withName: adaptor_removal {
beforeScript = "module purge; module load cutadapt/1.14" beforeScript = "module purge; module load cutadapt/1.14"
executor = "sge" executor = "sge"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128' queue = 'monointeldeb128'
} }
withName: trimming { withName: trimming {
...@@ -65,19 +65,23 @@ profiles { ...@@ -65,19 +65,23 @@ profiles {
cpus = 16 cpus = 16
memory = "5GB" memory = "5GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16' 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 { 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" beforeScript = "module purge; module load Bowtie2/2.3.4.1; module load sambamba/0.6.7; module load samblaster/0.6.7"
executor = "sge" executor = "sge"
cpus = 1 cpus = 1
memory = "30GB" memory = "30GB"
time = "6h" time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128' queue = 'monointeldeb128'
} }
withName: mapping_fastq { withName: mapping_fastq {
...@@ -86,8 +90,6 @@ profiles { ...@@ -86,8 +90,6 @@ profiles {
cpus = 16 cpus = 16
memory = "30GB" memory = "30GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16' penv = 'openmp16'
} }
...@@ -97,8 +99,6 @@ profiles { ...@@ -97,8 +99,6 @@ profiles {
cpus = 16 cpus = 16
memory = "30GB" memory = "30GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16' penv = 'openmp16'
} }
...@@ -108,8 +108,6 @@ profiles { ...@@ -108,8 +108,6 @@ profiles {
cpus = 16 cpus = 16
memory = "30GB" memory = "30GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16' penv = 'openmp16'
} }
...@@ -119,8 +117,6 @@ profiles { ...@@ -119,8 +117,6 @@ profiles {
cpus = 16 cpus = 16
memory = "30GB" memory = "30GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16' penv = 'openmp16'
} }
...@@ -130,8 +126,6 @@ profiles { ...@@ -130,8 +126,6 @@ profiles {
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128' queue = 'monointeldeb128'
} }
withName: index3_fasta { withName: index3_fasta {
...@@ -140,8 +134,6 @@ profiles { ...@@ -140,8 +134,6 @@ profiles {
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128' queue = 'monointeldeb128'
} }
withName: samtools_SNP_tumor { withName: samtools_SNP_tumor {
...@@ -150,8 +142,6 @@ profiles { ...@@ -150,8 +142,6 @@ profiles {
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128' queue = 'monointeldeb128'
} }
withName: samtools_SNP_norm { withName: samtools_SNP_norm {
...@@ -160,8 +150,6 @@ profiles { ...@@ -160,8 +150,6 @@ profiles {
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128' queue = 'monointeldeb128'
} }
withName: vcf_to_csv_tumor { withName: vcf_to_csv_tumor {
...@@ -170,8 +158,6 @@ profiles { ...@@ -170,8 +158,6 @@ profiles {
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128' queue = 'monointeldeb128'
} }
withName: vcf_to_csv_norm { withName: vcf_to_csv_norm {
...@@ -180,8 +166,6 @@ profiles { ...@@ -180,8 +166,6 @@ profiles {
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128' queue = 'monointeldeb128'
} }
} }
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment