diff --git a/src/arriba_fusion.nf b/src/arriba_fusion.nf index 474e5800c288f35a8f1618df2cf5051a74c32ec1..dc648e11732d25458f9c4a37fbe5b1c8a8c24626 100644 --- a/src/arriba_fusion.nf +++ b/src/arriba_fusion.nf @@ -77,9 +77,11 @@ params.design = "" params.genome = "/home/xavier/Data/Genome/hg19/Homo_sapiens.GRCh37.dna.primary_assembly.fa" params.cyto = "/home/xavier/Programs/arriba_v2.3.0/database/cytobands_hg19_hs37d5_GRCh37_v2.3.0.tsv" params.gtf = "/home/xavier/Data/Genome/hg19/Homo_sapiens.GRCh37.87.gtf" -params.index = "/home/xavier/Data/Genome/hg19/STAR" +//params.index = "/home/xavier/Data/Genome/hg19/STAR" +params.index = "" params.htseq_param = "yes" + /* Specific Arriba parameters */ params.arriba_options = "-f 'blacklist,read_through' \ -E 1 \ diff --git a/src/nextflow.config b/src/nextflow.config index ed18089184a57f8d348816627c1aa399bb28c633..b4c1642dee9d584400d5ff3d39fdcc39b6a7c173 100644 --- a/src/nextflow.config +++ b/src/nextflow.config @@ -125,6 +125,13 @@ profiles { time = "24h" clusterOptions = "--partition=Lake" } + withLabel: ultra_mem_multi_cpus { + executor = "slurm" + cpus = 32 + memory = "300GB" + time = "24h" + clusterOptions = "--partition=Lake" + } withLabel: small_mem_mono_cpus { executor = "slurm" cpus = 1 diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf index 8f5bd2512746893da78b5f1f48b1d9f176c76bd5..26f5d6a9b02c2637a35cae194cc37dac9fadc130 100644 --- a/src/nf_modules/star/main_2.7.8a.nf +++ b/src/nf_modules/star/main_2.7.8a.nf @@ -238,7 +238,7 @@ mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam process mapping2fusion { container = "${container_url}" - label "big_mem_multi_cpus" + label "ultra_mem_multi_cpus" tag "$reads_id" if (params.star_mapping2fusion_out != "") { publishDir "results/${params.star_mapping2fusion_out}", mode: 'copy'