From 299253e7b334996dded443c563be50cd694df2ed Mon Sep 17 00:00:00 2001 From: z483800 <109-z483800@users.noreply.gitlab.biologie.ens-lyon.fr> Date: Fri, 17 Jan 2020 14:30:41 +0000 Subject: [PATCH] Update src/RNAseq.config --- src/RNAseq.config | 53 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 src/RNAseq.config diff --git a/src/RNAseq.config b/src/RNAseq.config new file mode 100644 index 0000000..ed42799 --- /dev/null +++ b/src/RNAseq.config @@ -0,0 +1,53 @@ +profiles { + docker { + docker.temp = 'auto' + docker.enabled = true + process { + withName: adaptor_removal { + container = "lbmc/cutadapt:2.4" + cpus = 1 + } + } + } + singularity { + singularity.enabled = true + singularity.cacheDir = "./bin/" + process { + withName: adaptor_removal { + container = "lbmc/cutadapt:2.4" + cpus = 1 + } + } + } + psmn{ + process{ + withName: adaptor_removal { + 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 = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + } + } + } + ccin2p3 { + singularity.enabled = true + singularity.cacheDir = "$baseDir/.singularity_in2p3/" + singularity.runOptions = "--bind /pbs,/sps,/scratch" + process{ + withName: adaptor_removal { + container = "lbmc/cutadapt:2.4" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + queue = 'huge' + } + } + } +} -- GitLab