diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config index a8eb7758ef98d4e0097047417d58d6136a510e58..d17bc417d8e9b0cfac9d51cb5fa6e6c6776b62ea 100644 --- a/src/solution_RNASeq.config +++ b/src/solution_RNASeq.config @@ -109,6 +109,77 @@ profiles { } } } + psmn_singularity{ + singularity.enabled = true + singularity.cacheDir = "$baseDir/.singularity_psmn/" + singularity.runOptions = "--bind /Xnfs,/scratch" + process{ + withName: adaptor_removal { + container = "lbmc/cutadapt:2.1" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-cwd -V" + cpus = 1 + memory = "20GB" + time = "12h" + queue = "monointeldeb128" + } + withName: trimming { + container = "lbmc/urqt:d62c1f8" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-cwd -V" + cpus = 32 + memory = "30GB" + time = "24h" + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" + + } + withName: fasta_from_bed { + container = "lbmc/bedtools:2.25.0" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-cwd -V" + cpus = 1 + memory = "20GB" + time = "12h" + queue = "monointeldeb128" + } + withName: index_fasta { + container = "lbmc/kallisto:0.44.0" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-cwd -V" + cpus = 32 + memory = "30GB" + time = "24h" + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" + } + withName: mapping_fastq { + container = "lbmc/kallisto:0.44.0" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-cwd -V" + cpus = 32 + memory = "30GB" + time = "24h" + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" + } + } + } ccin2p3 { singularity.enabled = true singularity.cacheDir = "$baseDir/.singularity_in2p3/"