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 a297b91..72c9889 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 6aaed59..acc8e53 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 141819b..808e12a 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 f52e36a..a1b6add 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 4b87972..9d661f3 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 4b87972..9d661f3 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 8db956f..82ebc90 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 05836c4..8fe161a 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 05836c4..8fe161a 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 7d37077..b16c5d0 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 7d37077..b16c5d0 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 49dc99b..95919f5 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 84fe980..c52f9b5 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 b7c2ff4..2274d13 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 b7c2ff4..2274d13 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 ee43a05..f8ad13e 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 fff1d7b..d986c1f 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 abc81de..a6a2948 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 3114ab3..d6d0a90 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 86386ae..0801e38 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 86386ae..0801e38 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 5525c61..a000c5c 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 a87ad5b..c44c2e7 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 111683a..c0e08d0 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 e1f43fa..3ef8321 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 19937da..edd7856 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 ba68637..cc92880 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 ba68637..cc92880 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 d981cd3..5f176c6 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 d981cd3..5f176c6 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 b433677..984e336 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 b433677..984e336 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 ea511a0..6bbae43 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 6ad67ab..c60ee44 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 fe8e3ab..51afa4f 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 eeba96b..6aeaec5 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 3d804cc..b416751 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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