From 656b8f8d5e5ec927f9bd8ccb582375c9ac6d92d6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Thu, 28 Nov 2019 09:54:49 +0100
Subject: [PATCH] training_dataset.config: add ccin2p3 section
---
src/training_dataset.config | 129 ++++++++++++++++++++++++++++++++++++
1 file changed, 129 insertions(+)
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 453e7b7e..b122bd07 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -238,4 +238,133 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ process{
+ withName: build_synthetic_bed {
+ container = "lbmc/bedtools:2.25.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: index_fasta {
+ container = "lbmc/bowtie2:2.3.4.1"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: mapping_fastq_paired {
+ container = "lbmc/bowtie2:2.3.4.1"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: bam_2_fastq_paired {
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: sort_bam_paired {
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: index_bam_paired {
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: mapping_fastq_single {
+ container = "lbmc/bowtie2:2.3.4.1"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: bam_2_fastq_single {
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: sort_bam_single {
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: index_bam_single {
+ container = "lbmc/samtools:1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
--
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