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Verified Commit f8fe5b84 authored by Laurent Modolo's avatar Laurent Modolo
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nf modules singularity: remove logs for in2p3

parent f3591b54
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with 89 additions and 104 deletions
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
......@@ -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'
}
......
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