From 03f44eeff01896ba2b98d90dd350ab08e68d779e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 26 Oct 2018 16:17:30 +0200
Subject: [PATCH] nf modules config: remove cpus info
---
src/nf_modules/BEDtools/fasta_from_bed.config | 1 -
src/nf_modules/BWA/indexing.config | 1 -
src/nf_modules/BWA/mapping_paired.config | 1 -
src/nf_modules/Bowtie/indexing.config | 1 -
src/nf_modules/Bowtie/mapping_paired.config | 1 -
src/nf_modules/Bowtie/mapping_single.config | 1 -
src/nf_modules/Bowtie2/indexing.config | 8 +++-----
src/nf_modules/Bowtie2/mapping_paired.config | 1 -
src/nf_modules/Bowtie2/mapping_single.config | 1 -
src/nf_modules/FastQC/fastqc_paired.config | 1 -
src/nf_modules/FastQC/fastqc_single.config | 1 -
src/nf_modules/HTSeq/htseq.config | 2 --
src/nf_modules/Kallisto/indexing.config | 1 -
src/nf_modules/Kallisto/mapping_paired.config | 1 -
src/nf_modules/Kallisto/mapping_single.config | 1 -
src/nf_modules/MUSIC/peak_calling_single.config | 3 ---
src/nf_modules/MultiQC/multiqc_paired.config | 2 --
src/nf_modules/MultiQC/multiqc_single.config | 2 --
src/nf_modules/RSEM/indexing.config | 1 -
src/nf_modules/RSEM/quantification_paired.config | 1 -
src/nf_modules/RSEM/quantification_single.config | 1 -
src/nf_modules/SAMtools/filter_bams.config | 1 -
src/nf_modules/SAMtools/index_bams.config | 1 -
src/nf_modules/SAMtools/sort_bams.config | 1 -
src/nf_modules/SAMtools/split_bams.config | 1 -
src/nf_modules/SRAtoolkit/fastqdump.config | 1 -
src/nf_modules/UrQt/trimming_paired.config | 1 -
src/nf_modules/UrQt/trimming_single.config | 1 -
src/nf_modules/cutadapt/adaptor_removal_paired.config | 1 -
src/nf_modules/cutadapt/adaptor_removal_single.config | 1 -
src/nf_modules/cutadapt/trimming_paired.config | 1 -
src/nf_modules/cutadapt/trimming_single.config | 1 -
src/nf_modules/sambamba/index_bams.config | 1 -
src/nf_modules/sambamba/sort_bams.config | 1 -
src/nf_modules/sambamba/split_bams.config | 1 -
src/nf_modules/samblaster/dedup_sams.config | 1 -
src/training_dataset.config | 11 -----------
37 files changed, 3 insertions(+), 56 deletions(-)
diff --git a/src/nf_modules/BEDtools/fasta_from_bed.config b/src/nf_modules/BEDtools/fasta_from_bed.config
index a297b911..72c98899 100644
--- a/src/nf_modules/BEDtools/fasta_from_bed.config
+++ b/src/nf_modules/BEDtools/fasta_from_bed.config
@@ -15,7 +15,6 @@ profiles {
module = "BEDtools/2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/BWA/indexing.config b/src/nf_modules/BWA/indexing.config
index 6aaed59d..acc8e539 100644
--- a/src/nf_modules/BWA/indexing.config
+++ b/src/nf_modules/BWA/indexing.config
@@ -15,7 +15,6 @@ profiles {
module = "BWA/0.7.17"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "30GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/BWA/mapping_paired.config b/src/nf_modules/BWA/mapping_paired.config
index 141819be..808e12a6 100644
--- a/src/nf_modules/BWA/mapping_paired.config
+++ b/src/nf_modules/BWA/mapping_paired.config
@@ -15,7 +15,6 @@ profiles {
module = "BWA/0.7.17"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config
index f52e36ad..a1b6addd 100644
--- a/src/nf_modules/Bowtie/indexing.config
+++ b/src/nf_modules/Bowtie/indexing.config
@@ -15,7 +15,6 @@ profiles {
module = "Bowtie/1.2.2"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/Bowtie/mapping_paired.config b/src/nf_modules/Bowtie/mapping_paired.config
index 4b87972b..9d661f3f 100644
--- a/src/nf_modules/Bowtie/mapping_paired.config
+++ b/src/nf_modules/Bowtie/mapping_paired.config
@@ -15,7 +15,6 @@ profiles {
module = "Bowtie/1.2.2:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/Bowtie/mapping_single.config b/src/nf_modules/Bowtie/mapping_single.config
index 4b87972b..9d661f3f 100644
--- a/src/nf_modules/Bowtie/mapping_single.config
+++ b/src/nf_modules/Bowtie/mapping_single.config
@@ -15,7 +15,6 @@ profiles {
module = "Bowtie/1.2.2:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/Bowtie2/indexing.config b/src/nf_modules/Bowtie2/indexing.config
index 8db956f3..82ebc902 100644
--- a/src/nf_modules/Bowtie2/indexing.config
+++ b/src/nf_modules/Bowtie2/indexing.config
@@ -15,11 +15,9 @@ profiles {
module = "Bowtie2/2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
- memory = "30GB"
- time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
}
}
diff --git a/src/nf_modules/Bowtie2/mapping_paired.config b/src/nf_modules/Bowtie2/mapping_paired.config
index 05836c43..8fe161a0 100644
--- a/src/nf_modules/Bowtie2/mapping_paired.config
+++ b/src/nf_modules/Bowtie2/mapping_paired.config
@@ -15,7 +15,6 @@ profiles {
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/Bowtie2/mapping_single.config b/src/nf_modules/Bowtie2/mapping_single.config
index 05836c43..8fe161a0 100644
--- a/src/nf_modules/Bowtie2/mapping_single.config
+++ b/src/nf_modules/Bowtie2/mapping_single.config
@@ -15,7 +15,6 @@ profiles {
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/FastQC/fastqc_paired.config b/src/nf_modules/FastQC/fastqc_paired.config
index 7d37077b..b16c5d07 100644
--- a/src/nf_modules/FastQC/fastqc_paired.config
+++ b/src/nf_modules/FastQC/fastqc_paired.config
@@ -15,7 +15,6 @@ profiles {
module = "FastQC/0.11.5"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/FastQC/fastqc_single.config b/src/nf_modules/FastQC/fastqc_single.config
index 7d37077b..b16c5d07 100644
--- a/src/nf_modules/FastQC/fastqc_single.config
+++ b/src/nf_modules/FastQC/fastqc_single.config
@@ -15,7 +15,6 @@ profiles {
module = "FastQC/0.11.5"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/HTSeq/htseq.config b/src/nf_modules/HTSeq/htseq.config
index 49dc99b0..95919f56 100644
--- a/src/nf_modules/HTSeq/htseq.config
+++ b/src/nf_modules/HTSeq/htseq.config
@@ -18,7 +18,6 @@ profiles {
module = "SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -28,7 +27,6 @@ profiles {
module = "HTSeq/0.8.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/Kallisto/indexing.config b/src/nf_modules/Kallisto/indexing.config
index 84fe9803..c52f9b51 100644
--- a/src/nf_modules/Kallisto/indexing.config
+++ b/src/nf_modules/Kallisto/indexing.config
@@ -15,7 +15,6 @@ profiles {
module = "Kallisto/0.44.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/Kallisto/mapping_paired.config b/src/nf_modules/Kallisto/mapping_paired.config
index b7c2ff41..2274d13d 100644
--- a/src/nf_modules/Kallisto/mapping_paired.config
+++ b/src/nf_modules/Kallisto/mapping_paired.config
@@ -15,7 +15,6 @@ profiles {
module = "Kallisto/0.44.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/Kallisto/mapping_single.config b/src/nf_modules/Kallisto/mapping_single.config
index b7c2ff41..2274d13d 100644
--- a/src/nf_modules/Kallisto/mapping_single.config
+++ b/src/nf_modules/Kallisto/mapping_single.config
@@ -15,7 +15,6 @@ profiles {
module = "Kallisto/0.44.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/MUSIC/peak_calling_single.config b/src/nf_modules/MUSIC/peak_calling_single.config
index ee43a051..f8ad13e2 100644
--- a/src/nf_modules/MUSIC/peak_calling_single.config
+++ b/src/nf_modules/MUSIC/peak_calling_single.config
@@ -21,7 +21,6 @@ profiles {
module = "MUSIC/6613c53"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -31,7 +30,6 @@ profiles {
module = "MUSIC/6613c53"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -41,7 +39,6 @@ profiles {
module = "MUSIC/6613c53"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/MultiQC/multiqc_paired.config b/src/nf_modules/MultiQC/multiqc_paired.config
index fff1d7be..d986c1f0 100644
--- a/src/nf_modules/MultiQC/multiqc_paired.config
+++ b/src/nf_modules/MultiQC/multiqc_paired.config
@@ -19,7 +19,6 @@ profiles {
module = "FastQC/0.11.5"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
@@ -31,7 +30,6 @@ profiles {
module = "MultiQC/1.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
diff --git a/src/nf_modules/MultiQC/multiqc_single.config b/src/nf_modules/MultiQC/multiqc_single.config
index abc81de4..a6a2948a 100644
--- a/src/nf_modules/MultiQC/multiqc_single.config
+++ b/src/nf_modules/MultiQC/multiqc_single.config
@@ -18,7 +18,6 @@ profiles {
module = "FastQC/0.11.5"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
@@ -30,7 +29,6 @@ profiles {
module = "MultiQC/1.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
diff --git a/src/nf_modules/RSEM/indexing.config b/src/nf_modules/RSEM/indexing.config
index 3114ab31..d6d0a908 100644
--- a/src/nf_modules/RSEM/indexing.config
+++ b/src/nf_modules/RSEM/indexing.config
@@ -15,7 +15,6 @@ profiles {
module = "RSEM/1.3.0:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/RSEM/quantification_paired.config b/src/nf_modules/RSEM/quantification_paired.config
index 86386ae0..0801e388 100644
--- a/src/nf_modules/RSEM/quantification_paired.config
+++ b/src/nf_modules/RSEM/quantification_paired.config
@@ -15,7 +15,6 @@ profiles {
module = "RSEM/1.3.0:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/RSEM/quantification_single.config b/src/nf_modules/RSEM/quantification_single.config
index 86386ae0..0801e388 100644
--- a/src/nf_modules/RSEM/quantification_single.config
+++ b/src/nf_modules/RSEM/quantification_single.config
@@ -15,7 +15,6 @@ profiles {
module = "RSEM/1.3.0:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/SAMtools/filter_bams.config b/src/nf_modules/SAMtools/filter_bams.config
index 5525c61f..a000c5cd 100644
--- a/src/nf_modules/SAMtools/filter_bams.config
+++ b/src/nf_modules/SAMtools/filter_bams.config
@@ -15,7 +15,6 @@ profiles {
module = "SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/SAMtools/index_bams.config b/src/nf_modules/SAMtools/index_bams.config
index a87ad5bf..c44c2e73 100644
--- a/src/nf_modules/SAMtools/index_bams.config
+++ b/src/nf_modules/SAMtools/index_bams.config
@@ -15,7 +15,6 @@ profiles {
module = "SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/SAMtools/sort_bams.config b/src/nf_modules/SAMtools/sort_bams.config
index 111683a2..c0e08d02 100644
--- a/src/nf_modules/SAMtools/sort_bams.config
+++ b/src/nf_modules/SAMtools/sort_bams.config
@@ -15,7 +15,6 @@ profiles {
module = "SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/SAMtools/split_bams.config b/src/nf_modules/SAMtools/split_bams.config
index e1f43fa9..3ef8321e 100644
--- a/src/nf_modules/SAMtools/split_bams.config
+++ b/src/nf_modules/SAMtools/split_bams.config
@@ -15,7 +15,6 @@ profiles {
module = "SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/SRAtoolkit/fastqdump.config b/src/nf_modules/SRAtoolkit/fastqdump.config
index 19937da5..edd7856a 100644
--- a/src/nf_modules/SRAtoolkit/fastqdump.config
+++ b/src/nf_modules/SRAtoolkit/fastqdump.config
@@ -15,7 +15,6 @@ profiles {
module = "SRAtoolkit/2.8.2"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/UrQt/trimming_paired.config b/src/nf_modules/UrQt/trimming_paired.config
index ba68637b..cc928803 100644
--- a/src/nf_modules/UrQt/trimming_paired.config
+++ b/src/nf_modules/UrQt/trimming_paired.config
@@ -15,7 +15,6 @@ profiles {
module = "UrQt/d62c1f8"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "5GB"
time = "12h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/UrQt/trimming_single.config b/src/nf_modules/UrQt/trimming_single.config
index ba68637b..cc928803 100644
--- a/src/nf_modules/UrQt/trimming_single.config
+++ b/src/nf_modules/UrQt/trimming_single.config
@@ -15,7 +15,6 @@ profiles {
module = "UrQt/d62c1f8"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "5GB"
time = "12h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index d981cd30..5f176c68 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -15,7 +15,6 @@ profiles {
module = "cutadapt/1.14"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index d981cd30..5f176c68 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -15,7 +15,6 @@ profiles {
module = "cutadapt/1.14"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index b433677f..984e336a 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -15,7 +15,6 @@ profiles {
module = "cutadapt/1.14"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index b433677f..984e336a 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -15,7 +15,6 @@ profiles {
module = "cutadapt/1.14"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index ea511a0b..6bbae437 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -15,7 +15,6 @@ profiles {
module = "sambamba/0.6.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 6ad67ab0..c60ee44e 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -15,7 +15,6 @@ profiles {
module = "sambamba/0.6.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index fe8e3ab8..51afa4fa 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -15,7 +15,6 @@ profiles {
module = "sambamba/0.6.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index eeba96b2..6aeaec5f 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -15,7 +15,6 @@ profiles {
module = "samblaster/0.1.24"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 3d804cca..b416751d 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -45,7 +45,6 @@ profiles {
module = "BEDtools/2.25.0"
executor = "sge"
clusterOptions = "-m be -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -55,7 +54,6 @@ profiles {
module = "BEDtools/2.25.0"
executor = "sge"
clusterOptions = "-m be -cwd -V"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -64,7 +62,6 @@ profiles {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1"
executor = "sge"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
@@ -74,7 +71,6 @@ profiles {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
executor = "sge"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
@@ -84,7 +80,6 @@ profiles {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -93,7 +88,6 @@ profiles {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -102,7 +96,6 @@ profiles {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -111,7 +104,6 @@ profiles {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
executor = "sge"
- cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
@@ -121,7 +113,6 @@ profiles {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -130,7 +121,6 @@ profiles {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
@@ -139,7 +129,6 @@ profiles {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
- cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
--
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