From f8fe5b84dbe5abcf155a18fd5d3e797ed85401fb Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 21 May 2019 14:15:33 +0200
Subject: [PATCH] nf modules singularity: remove logs for in2p3
---
src/nf_modules/bedtools/fasta_from_bed.config | 9 +++--
src/nf_modules/bowtie/indexing.config | 9 +++--
src/nf_modules/bowtie/mapping_paired.config | 9 +++--
src/nf_modules/bowtie/mapping_single.config | 9 +++--
src/nf_modules/bowtie2/indexing.config | 9 +++--
src/nf_modules/bowtie2/mapping_paired.config | 9 +++--
src/nf_modules/bowtie2/mapping_single.config | 9 +++--
src/nf_modules/bwa/indexing.config | 9 +++--
src/nf_modules/bwa/mapping_paired.config | 9 +++--
.../cutadapt/adaptor_removal_paired.config | 9 +++--
.../cutadapt/adaptor_removal_single.config | 9 +++--
.../cutadapt/trimming_paired.config | 8 ++---
.../cutadapt/trimming_single.config | 8 ++---
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 | 10 +++---
src/nf_modules/fastp/fastp_single.config | 10 +++---
src/nf_modules/fastqc/fastqc_paired.config | 10 +++---
src/nf_modules/fastqc/fastqc_single.config | 10 +++---
src/nf_modules/hisat2/indexing.config | 10 +++---
src/nf_modules/hisat2/mapping_paired.config | 8 ++---
src/nf_modules/hisat2/mapping_single.config | 8 ++---
src/nf_modules/htseq/htseq.config | 18 +++++-----
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 | 18 +++++-----
src/nf_modules/multiqc/multiqc_single.config | 18 +++++-----
.../music/peak_calling_single.config | 36 +++++++++----------
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 | 10 +++---
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 | 10 +++---
src/nf_modules/samtools/sort_bams.config | 10 +++---
src/nf_modules/samtools/split_bams.config | 10 +++---
src/nf_modules/sratoolkit/fastqdump.config | 10 +++---
src/nf_modules/urqt/trimming_paired.config | 10 +++---
src/nf_modules/urqt/trimming_single.config | 10 +++---
45 files changed, 237 insertions(+), 252 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 41c1dac9..1a225212 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fasta_from_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 73217f9a..06b57209 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 44ab8bcb..61f40f9e 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 44ab8bcb..61f40f9e 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 20487563..2d52dc48 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 7874ae45..85655e48 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 7874ae45..85655e48 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 72274ad4..c970b5bb 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index a3e5c628..af4f9683 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index e58c385a..8add46ca 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index e58c385a..8add46ca 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 9b49fcee..721d8805 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
@@ -58,8 +57,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 9b49fcee..721d8805 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
@@ -58,8 +57,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 67a46dc8..5be6a4cb 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -26,7 +26,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -61,8 +61,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -73,8 +73,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -90,8 +90,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -101,8 +101,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index fb1cd048..b0986769 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: compute_matrix {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 08d20977..e9fe1504 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: plot_profile {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 7d9c83e4..df041cb9 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastp_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 7d9c83e4..df041cb9 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastp_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 6e9dcaf7..2ed15c54 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 6e9dcaf7..2ed15c54 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 6d39e60a..d97e7c74 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 97b4807d..c0b9c808 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 97b4807d..c0b9c808 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 09b368ae..c8f844e9 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -22,7 +22,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -55,8 +55,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -67,8 +67,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -84,8 +84,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -95,8 +95,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 84722f6d..b677b616 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 801dfdc1..620e506d 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 801dfdc1..620e506d 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 93697c70..8e3965f8 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: peak_calling {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 86ead2c4..1825a135 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -27,7 +27,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -64,8 +64,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -76,8 +76,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -93,8 +93,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -104,8 +104,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index e296853f..6a2edfb6 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -26,7 +26,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -63,8 +63,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -75,8 +75,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -92,8 +92,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -103,8 +103,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 972de3d7..dc46d8c8 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -11,7 +11,7 @@ profiles {
container = "music:6613c53"
cpus = 1
}
- withName: music_computation {
+ withName: music_computation{
container = "music:6613c53"
cpus = 1
}
@@ -28,13 +28,13 @@ profiles {
container = "file://bin/music:6613c53.img"
cpus = 1
}
- withName: music_computation {
+ withName: music_computation{
container = "file://bin/music:6613c53.img"
cpus = 1
}
}
}
- psmn {
+ psmn{
process{
withName: compute_mappability {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -56,7 +56,7 @@ profiles {
time = "12h"
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
- withName: music_computation {
+ withName: music_computation{
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "music/6613c53"
executor = "sge"
@@ -77,8 +77,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -89,20 +89,20 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
- withName: music_computation {
+ withName: music_computation{
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -118,8 +118,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -129,19 +129,19 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
- withName: music_computation {
+ withName: music_computation{
container = "/sps/lbmc/common/singularity/music:6613c53.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index b9de2536..d58a310d 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 03152cca..75aae6ed 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 03152cca..75aae6ed 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index cb3d4308..9199b7a4 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index de2eb6e8..0a71fc38 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 74dd96d0..8a3e4ab5 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: split_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index a47c35ac..7fd05167 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: dedup_sam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index dfc5d68f..fc7a216c 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: filter_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 3c0e876c..8b910b60 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 690dc903..d5e06e31 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 6afd8880..c145bf33 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: split_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 6abc3955..0d5acb9f 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastq_dump {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 976921f2..dbe4e11c 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 99fb7d94..016d6503 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
--
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