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Unverified Commit 670315f5 authored by Laurent Modolo's avatar Laurent Modolo
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nf_modules: switch psmn to singularity

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src/.update_config.sh
+ 3
− 1
View file @ 670315f5
......@@ -25,4 +25,6 @@ fd ".*config" src/ -x perl -0777pe 's|openmp16|openmp32|mg' -i {}
fd ".*config" src/ -x perl -0777pe 's|cpus = 16|cpus = 32|mg' -i {}
fd ".*config" src/ -x perl -0777pe "s|'|\"|mg" -i {}
# we update the psmn config to singularity
fd ".*config" src/ -x perl -0777pe 's|psmn{|psmn{\n singularity.enabled = true\n singularity.cacheDir = "$baseDir/.singularity_psmn/"\n singularity.runOptions = "--bind /Xnfs,/scratch"|mg' -i {}
fd ".*config" src/ -x perl -0777pe 's|beforeScript.*conda.*(\n\s*clusterOptions = "-cwd -V".*)(container .*executor = "sge")|\2\1\2|gs' -i {}
src/nf_modules/bedtools/fasta_from_bed.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fasta_from_bed {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bedtools_2.25.0"
container = "lbmc/bedtools:2.25.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/bowtie/indexing.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie_1.2.2"
container = "lbmc/bowtie:1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
......
src/nf_modules/bowtie/mapping_paired.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie/1.2.2"
container = "lbmc/bowtie:1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/bowtie/mapping_single.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie/1.2.2"
container = "lbmc/bowtie:1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/bowtie2/indexing.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
container = "lbmc/bowtie2:2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/bowtie2/mapping_paired.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
container = "lbmc/bowtie2:2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/bowtie2/mapping_single.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
container = "lbmc/bowtie2:2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/bwa/indexing.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bwa_0.7.17"
container = "lbmc/bwa:0.7.17"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/bwa/mapping_paired.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bwa_0.7.17"
container = "lbmc/bwa:0.7.17"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/cutadapt/adaptor_removal_paired.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: adaptor_removal {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.4"
container = "lbmc/cutadapt:2.4"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/cutadapt/adaptor_removal_single.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: adaptor_removal {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.4"
container = "lbmc/cutadapt:2.4"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/cutadapt/trimming_paired.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.4"
container = "lbmc/cutadapt:2.4"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/cutadapt/trimming_single.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.4"
container = "lbmc/cutadapt:2.4"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/deeptools/bam_to_bigwig.config
+ 7
− 13
View file @ 670315f5
......@@ -28,21 +28,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_bam {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/sambamba_0.6.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
memory = "30GB"
time = "24h"
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"
container = "lbmc/deeptools:3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/deeptools/compute_matrix.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: compute_matrix {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/deeptools_3.0.2"
container = "lbmc/deeptools:3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/deeptools/plot_profile.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: plot_profile {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/deeptools_3.0.2"
container = "lbmc/deeptools:3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
......
src/nf_modules/fastp/fastp_paired.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastp_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/fastp_0.19.7"
container = "lbmc/fastp:0.19.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/fastp/fastp_single.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastp_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/fastp_0.19.7"
container = "lbmc/fastp:0.19.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/fastqc/fastqc_paired.config
+ 7
− 2
View file @ 670315f5
......@@ -20,10 +20,15 @@ profiles {
}
}
psmn{
singularity.enabled = true
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/fastqc_0.11.5"
container = "lbmc/fastqc:0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
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