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Commit f60f93c4 authored by elabaron's avatar elabaron
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src/RNAseq.config : change conda env in singularity in psmn profile

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profiles { profiles {
sge { psmn {
singularity.enabled = true
singularity.cacheDir = "$baseDir/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{ process{
withName: fastqc_raw { withName: fastqc_raw {
beforeScript = "source $baseDir/.conda_psmn.sh" container = "lbmc/fastqc:0.11.5"
conda = "$baseDir/.conda_envs/fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 4
penv = 'openmp4'
memory = "20GB"
time = "12h"
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
}
withName: trimming {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.4"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
}
withName: fastqc_cut {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/fastqc_0.11.5"
executor = "sge" executor = "sge"
clusterOptions = "-cwd -V" clusterOptions = "-cwd -V"
cpus = 4 cpus = 4
...@@ -33,88 +14,109 @@ profiles { ...@@ -33,88 +14,109 @@ profiles {
time = "12h" time = "12h"
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
} }
withName: trimming {
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
}
withName: fastqc_cut {
container = "lbmc/fastqc:0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 4
penv = 'openmp4'
memory = "20GB"
time = "12h"
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
}
withName: rRNA_removal { withName: rRNA_removal {
beforeScript = "source $baseDir/.conda_psmn.sh" container = "lbmc/bowtie2:2.3.4.1"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge"
executor = "sge" clusterOptions = "-cwd -V"
clusterOptions = "-cwd -V" queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' penv = 'openmp8'
penv = 'openmp8' cpus = 8
cpus = 8
} }
withName: fastqc_filter { withName: fastqc_filter {
beforeScript = "source $baseDir/.conda_psmn.sh" container = "lbmc/fastqc:0.11.5"
conda = "$baseDir/.conda_envs/fastqc_0.11.5" executor = "sge"
executor = "sge" clusterOptions = "-cwd -V"
clusterOptions = "-cwd -V" cpus = 4
cpus = 4 penv = 'openmp4'
penv = 'openmp4' memory = "20GB"
memory = "20GB" time = "12h"
time = "12h" queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
} }
withName: hisat2_genome { withName: hisat2_genome {
beforeScript = "source $baseDir/.conda_psmn.sh" container = "lbmc/hisat2:2.1.0"
conda = "$baseDir/.conda_envs/hisat2_2.1.0" executor = "sge"
executor = "sge" clusterOptions = "-cwd -V"
clusterOptions = "-cwd -V" memory = "20GB"
memory = "20GB" cpus = 16
cpus = 16 penv = 'openmp16'
penv = 'openmp16' time = "12h"
time = "12h" queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' penv = 'openmp16'
penv = 'openmp16'
} }
withName: fastqc_genome { withName: fastqc_genome {
beforeScript = "source $baseDir/.conda_psmn.sh" container = "lbmc/fastqc:0.11.5"
conda = "$baseDir/.conda_envs/fastqc_0.11.5" executor = "sge"
executor = "sge" clusterOptions = "-cwd -V"
clusterOptions = "-cwd -V" cpus = 4
cpus = 4 penv = 'openmp4'
penv = 'openmp4' memory = "20GB"
memory = "20GB" time = "12h"
time = "12h" queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
} }
withName: dedup_genome { withName: dedup_genome {
beforeScript = "source $baseDir/.cond a_psmn.sh" container = "lbmc/umi_tools:1.0.0"
conda = "$baseDir/.conda_envs/umitools_0.3.4" executor = "sge"
executor = "sge" clusterOptions = "-cwd -V"
clusterOptions = "-cwd -V" cpus = 1
cpus = 1 memory = "20GB"
memory = "20GB" time = "12h"
time = "12h" queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
} }
withName: sort_bam { withName: sort_bam {
beforeScript = "source $baseDir/.conda_psmn.sh" container = "lbmc/hisat2:2.1.0"
conda = "$baseDir/.conda_envs/hisat2_2.1.0" executor = "sge"
executor = "sge" clusterOptions = "-cwd -V"
clusterOptions = "-cwd -V" cpus = 8
cpus = 8 penv = 'openmp8'
penv = 'openmp8' memory = "20GB"
memory = "20GB" time = "12h"
time = "12h" queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
} }
withName: counting { withName: counting {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules; module purge; module load htseq/0.11.2" container = "lbmc/htseq:0.11.2"
executor = "sge" executor = "sge"
clusterOptions = "-cwd -V" clusterOptions = "-cwd -V"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
} }
withName: multiqc { withName: multiqc {
beforeScript = "source $baseDir/.conda_psmn.sh" container = "ewels/multiqc:1.9"
conda = "$baseDir/.conda_envs/multiqc_1.7" executor = "sge"
executor = "sge" clusterOptions = "-cwd -V"
clusterOptions = "-cwd -V" cpus = 1
cpus = 1 memory = "20GB"
memory = "20GB" time = "12h"
time = "12h" queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' }
withName: rnaseq_qc {
container = "gcr.io/broad-cga-aarong-gtex/rnaseqc:latest"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
} }
} }
} }
......
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