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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

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with 123 additions and 123 deletions
src/nf_modules/hisat2/indexing.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/hisat2/mapping_paired.config
+ 4
− 4
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/hisat2/mapping_single.config
+ 4
− 4
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/htseq/htseq.config
+ 9
− 9
View file @ f8fe5b84
......@@ -56,7 +56,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -68,7 +68,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -85,7 +85,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -96,7 +96,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/kallisto/indexing.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/kallisto/mapping_paired.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/kallisto/mapping_single.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/macs2/peak_calling.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/multiqc/multiqc_paired.config
+ 9
− 9
View file @ f8fe5b84
......@@ -65,7 +65,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -77,7 +77,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -94,7 +94,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -105,7 +105,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/multiqc/multiqc_single.config
+ 9
− 9
View file @ f8fe5b84
......@@ -64,7 +64,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -76,7 +76,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -93,7 +93,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -104,7 +104,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/music/peak_calling_single.config
+ 18
− 18
View file @ f8fe5b84
......@@ -78,7 +78,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -90,7 +90,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -102,7 +102,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -119,7 +119,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -130,7 +130,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -141,7 +141,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/rsem/indexing.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/rsem/quantification_paired.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/rsem/quantification_single.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/sambamba/index_bams.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/sambamba/sort_bams.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/sambamba/split_bams.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/samblaster/dedup_sams.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/samtools/filter_bams.config
+ 5
− 5
View file @ f8fe5b84
......@@ -43,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -60,7 +60,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
src/nf_modules/samtools/index_bams.config
+ 5
− 5
View file @ f8fe5b84
......@@ -42,7 +42,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......@@ -59,7 +59,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-o ~/logs/ -e ~/logs/"
"
cpus = 1
queue = 'huge'
}
......
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