From c116038b3d0e802c2528384ff0a1656ad3b29529 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 17 Apr 2020 16:06:45 +0200
Subject: [PATCH] update psmn config to new queues
---
src/.update_config.sh | 6 ++
src/nf_modules/bedtools/fasta_from_bed.config | 6 +-
src/nf_modules/bowtie/indexing.config | 10 +--
src/nf_modules/bowtie/mapping_paired.config | 10 +--
src/nf_modules/bowtie/mapping_single.config | 10 +--
src/nf_modules/bowtie2/indexing.config | 10 +--
src/nf_modules/bowtie2/mapping_paired.config | 10 +--
src/nf_modules/bowtie2/mapping_single.config | 10 +--
src/nf_modules/bwa/indexing.config | 10 +--
src/nf_modules/bwa/mapping_paired.config | 10 +--
.../cutadapt/adaptor_removal_paired.config | 6 +-
.../cutadapt/adaptor_removal_single.config | 6 +-
.../cutadapt/trimming_paired.config | 6 +-
.../cutadapt/trimming_single.config | 6 +-
src/nf_modules/deeptools/bam_to_bigwig.config | 18 ++--
.../deeptools/compute_matrix.config | 10 +--
src/nf_modules/deeptools/plot_profile.config | 10 +--
src/nf_modules/fastp/fastp_paired.config | 6 +-
src/nf_modules/fastp/fastp_single.config | 6 +-
src/nf_modules/fastqc/fastqc_paired.config | 6 +-
src/nf_modules/fastqc/fastqc_single.config | 6 +-
src/nf_modules/hisat2/indexing.config | 10 +--
src/nf_modules/hisat2/mapping_paired.config | 10 +--
src/nf_modules/hisat2/mapping_single.config | 10 +--
src/nf_modules/htseq/htseq.config | 10 +--
src/nf_modules/kallisto/indexing.config | 10 +--
src/nf_modules/kallisto/mapping_paired.config | 10 +--
src/nf_modules/kallisto/mapping_single.config | 10 +--
src/nf_modules/macs2/peak_calling.config | 10 +--
src/nf_modules/multiqc/multiqc_paired.config | 14 ++--
src/nf_modules/multiqc/multiqc_single.config | 14 ++--
.../music/peak_calling_single.config | 14 ++--
src/nf_modules/rsem/indexing.config | 10 +--
.../rsem/quantification_paired.config | 10 +--
.../rsem/quantification_single.config | 10 +--
src/nf_modules/sambamba/index_bams.config | 10 +--
src/nf_modules/sambamba/sort_bams.config | 8 +-
src/nf_modules/sambamba/split_bams.config | 10 +--
src/nf_modules/samblaster/dedup_sams.config | 10 +--
src/nf_modules/samtools/filter_bams.config | 10 +--
src/nf_modules/samtools/index_bams.config | 6 +-
src/nf_modules/samtools/sort_bams.config | 10 +--
src/nf_modules/samtools/split_bams.config | 6 +-
src/nf_modules/sratoolkit/fastqdump.config | 6 +-
src/nf_modules/star/indexing.config | 10 +--
src/nf_modules/star/mapping_paired.config | 10 +--
src/nf_modules/star/mapping_single.config | 10 +--
src/nf_modules/subread/subread.config | 10 +--
src/nf_modules/urqt/trimming_paired.config | 10 +--
src/nf_modules/urqt/trimming_single.config | 10 +--
src/solution_RNASeq.config | 28 +++----
src/training_dataset.config | 84 +++++++++----------
52 files changed, 292 insertions(+), 286 deletions(-)
diff --git a/src/.update_config.sh b/src/.update_config.sh
index 3e7c6a1e..c591051e 100644
--- a/src/.update_config.sh
+++ b/src/.update_config.sh
@@ -17,3 +17,9 @@ fd ".*config" -E "nf_modules" src/ -x perl -0777pe "s|\s*ccin2p3_conda {.*ccin2p
# we update the psmn module to conda
fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"\n\s*module = "(.*)/(.*)"|beforeScript = "source \$baseDir/.conda_psmn.sh"\n conda = "\$baseDir/.conda_envs/\L\1_\2"|mg' -i {}
+
+# we update the psmn queue to new cluster
+fd ".*config" src/ -x perl -0777pe 's|E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F|CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D|mg' -i {}
+fd ".*config" src/ -x perl -0777pe 's|monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128|monointeldeb128|mg' -i {}
+fd ".*config" src/ -x perl -0777pe 's|openmp16|openmp32|mg' -i {}
+fd ".*config" src/ -x perl -0777pe 's|cpus = 16|cpus = 32|mg' -i {}
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 7a3302d7..7642dec3 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fasta_from_bed {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -46,7 +46,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index c67cef25..0fa19189 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -27,10 +27,10 @@ profiles {
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index ac4c35e4..b29cc8de 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/bowtie/1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index ac4c35e4..b29cc8de 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/bowtie/1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index dd1e5e06..2f37d692 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "20GB"
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index c4b0fdd1..155b3668 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index c4b0fdd1..155b3668 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 689b5fa2..12adc8e6 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/bwa_0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index b2e198a0..7fce44a3 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/bwa_0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index ed42799d..30b344cd 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: adaptor_removal {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -46,7 +46,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index ed42799d..30b344cd 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: adaptor_removal {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -46,7 +46,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 8c158c0e..397c7f5c 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: trimming {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -46,7 +46,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 8c158c0e..397c7f5c 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: trimming {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -46,7 +46,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 2cbf9d68..6d26a3e5 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_bam {
@@ -34,22 +34,22 @@ profiles {
conda = "$baseDir/.conda_envs/sambamba_0.6.7"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: bam_to_bigwig {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "deeptools/3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -67,7 +67,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: bam_to_bigwig {
container = "lbmc/deeptools:3.0.2"
@@ -78,7 +78,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index d1c05456..5a8c4135 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: compute_matrix {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/deeptools_3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index c10e0edc..67b36ba4 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: plot_profile {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/deeptools_3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index d2ef420f..becedca3 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastp_fastq {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +47,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index d2ef420f..becedca3 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastp_fastq {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +47,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 743c85ec..eddcc94b 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastqc_fastq {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +47,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 743c85ec..eddcc94b 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastqc_fastq {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +47,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index ab38148c..e726418f 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -27,10 +27,10 @@ profiles {
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index b3e4df57..964db521 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -27,10 +27,10 @@ profiles {
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index b3e4df57..964db521 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -27,10 +27,10 @@ profiles {
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 2eebc16c..40f27a3a 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: sort_bam {
@@ -37,7 +37,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
withName: counting {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -47,7 +47,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -65,7 +65,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: counting {
container = "lbmc/htseq:0.11.2"
@@ -76,7 +76,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 3ca188a0..14dd1ade 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName index_fasta {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 04b61fea..7fdd1dcd 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 04b61fea..7fdd1dcd 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 35186c52..7c4c8500 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: peak_calling {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/macs2_2.1.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 1cb17b7c..d0202652 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -1,7 +1,7 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastqc_fastq {
@@ -39,8 +39,8 @@ profiles {
memory = "5GB"
time = "6h"
queueSize = 1.70
- pollInterval = '60sec'
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ pollInterval = "60sec"
+ queue = "monointeldeb128"
}
withName: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -51,8 +51,8 @@ profiles {
memory = "5GB"
time = "6h"
queueSize = 1.70
- pollInterval = '60sec'
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ pollInterval = "60sec"
+ queue = "monointeldeb128"
}
}
}
@@ -70,7 +70,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: multiqc {
container = "lbmc/multiqc:1.7"
@@ -81,7 +81,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index ba1bbe7c..301dde8b 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastqc_fastq {
@@ -38,8 +38,8 @@ profiles {
memory = "5GB"
time = "6h"
queueSize = 1.70
- pollInterval = '60sec'
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ pollInterval = "60sec"
+ queue = "monointeldeb128"
}
withName: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -50,8 +50,8 @@ profiles {
memory = "5GB"
time = "6h"
queueSize = 1.70
- pollInterval = '60sec'
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ pollInterval = "60sec"
+ queue = "monointeldeb128"
}
}
}
@@ -69,7 +69,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: multiqc {
container = "lbmc/multiqc:1.7"
@@ -80,7 +80,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 4a500bb9..0372788c 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: compute_mappability {
@@ -45,7 +45,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
withName: music_preprocessing {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -55,7 +55,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
withName: music_computation{
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -65,7 +65,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -83,7 +83,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: music_preprocessing {
container = "lbmc/music:6613c53"
@@ -94,7 +94,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: music_computation{
container = "lbmc/music:6613c53"
@@ -105,7 +105,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index d5d3c781..c2c06001 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/rsem_1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index bde03fc9..fd73ae66 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/rsem_1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index bde03fc9..fd73ae66 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/rsem_1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 3a20b7e1..c3d12b70 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_bam {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/sambamba_0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 8612de4a..1db926f7 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: sort_bam {
@@ -29,8 +29,8 @@ profiles {
cpus = 4
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 4ce0bcb0..1ec31c3e 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: split_bam {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/sambamba_0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 66f30511..10c1649e 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: dedup_sam {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/samblaster_0.1.24"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index b2cdd8e5..46933f1d 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: filter_bam {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 3e2156e1..438f8379 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_bam {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +47,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index dd7cd38b..81371fb5 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: sort_bam {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 6c8ca3e9..837fe88d 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: split_bam {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +47,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index e6e80c5d..4c651697 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastq_dump {
@@ -29,7 +29,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +47,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
index 34683657..cef16406 100644
--- a/src/nf_modules/star/indexing.config
+++ b/src/nf_modules/star/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/star_2.7.3a"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "20GB"
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
index 615404c4..6f8f8048 100644
--- a/src/nf_modules/star/mapping_paired.config
+++ b/src/nf_modules/star/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/star_2.7.3a"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
index 615404c4..6f8f8048 100644
--- a/src/nf_modules/star/mapping_single.config
+++ b/src/nf_modules/star/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/star_2.7.3a"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +47,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 68147001..ef2aa7e5 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: sort_bam {
@@ -37,7 +37,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
withName: counting {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -47,7 +47,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -65,7 +65,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: counting {
container = "lbmc/subread:1.6.4"
@@ -76,7 +76,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index a9f28632..87f7f7f9 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: trimming {
@@ -27,10 +27,10 @@ profiles {
executor = "sge"
clusterOptions = "-cwd -V"
memory = "5GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 012b3f3a..c2b5757e 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: trimming {
@@ -26,11 +26,11 @@ profiles {
conda = "$baseDir/.conda_envs/urqt_d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "5GB"
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config
index 3e8ba47b..a8eb7758 100644
--- a/src/solution_RNASeq.config
+++ b/src/solution_RNASeq.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: adaptor_removal {
@@ -61,7 +61,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128'
+ queue = "monointeldeb128"
}
withName: trimming {
beforeScript = "source $baseDir/.conda_psmn.sh"
@@ -71,8 +71,8 @@ profiles {
cpus = 32
memory = "30GB"
time = "24h"
- queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
- penv = 'openmp32'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: fasta_from_bed {
@@ -83,7 +83,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128'
+ queue = "monointeldeb128"
}
withName: index_fasta {
beforeScript = "source $baseDir/.conda_psmn.sh"
@@ -93,8 +93,8 @@ profiles {
cpus = 32
memory = "30GB"
time = "24h"
- queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
- penv = 'openmp32'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: mapping_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
@@ -104,8 +104,8 @@ profiles {
cpus = 32
memory = "30GB"
time = "24h"
- queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
- penv = 'openmp32'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -122,7 +122,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: trimming {
container = "lbmc/urqt:d62c1f8"
@@ -133,7 +133,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
@@ -143,7 +143,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
@@ -154,7 +154,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
@@ -165,7 +165,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 226acd9f..734a7410 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: build_synthetic_bed {
@@ -125,7 +125,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
withName: fasta_from_bed {
beforeScript = "source $baseDir/.conda_psmn.sh"
@@ -135,106 +135,106 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
withName: index_fasta {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "20GB"
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: mapping_fastq_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: bam_2_fastq_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: sort_bam_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: index_bam_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: mapping_fastq_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: bam_2_fastq_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: sort_bam_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: index_bam_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -251,7 +251,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
process{
@@ -263,7 +263,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
@@ -273,7 +273,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: index_fasta {
container = "lbmc/bowtie2:2.3.4.1"
@@ -283,7 +283,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: mapping_fastq_paired {
container = "lbmc/bowtie2:2.3.4.1"
@@ -293,7 +293,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: bam_2_fastq_paired {
container = "lbmc/samtools:1.7"
@@ -303,7 +303,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: sort_bam_paired {
container = "lbmc/samtools:1.7"
@@ -313,7 +313,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: index_bam_paired {
container = "lbmc/samtools:1.7"
@@ -323,7 +323,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: mapping_fastq_single {
container = "lbmc/bowtie2:2.3.4.1"
@@ -333,7 +333,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: bam_2_fastq_single {
container = "lbmc/samtools:1.7"
@@ -343,7 +343,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: sort_bam_single {
container = "lbmc/samtools:1.7"
@@ -353,7 +353,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: index_bam_single {
container = "lbmc/samtools:1.7"
@@ -363,7 +363,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
--
GitLab