diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config index df2f3a2..46d95a5 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -4,18 +4,25 @@ params { config_profile_contact = 'Maxime Garcia (@MaxUlysse)' config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs' - singleCPUmem = 7000.MB + single_cpu_mem = 7000.MB // Just useful until iGenomes is updated on UPPMAX - igenomeIgnore = true + igenomes_ignore = true genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle' } def hostname = "hostname".execute().text.trim() if (hostname ==~ "r.*") { - params.singleCPUmem = 6400.MB + params.single_cpu_mem = 6400.MB + + process { + withName:BamQC { + cpus = {params.max_cpus} + memory = {params.max_memory} + } + } } if (hostname ==~ "i.*") { - params.singleCPUmem = 15.GB + params.single_cpu_mem = 15.GB } diff --git a/conf/uppmax.config b/conf/uppmax.config index 037070a..bc3d8c4 100644 --- a/conf/uppmax.config +++ b/conf/uppmax.config @@ -15,7 +15,7 @@ process { } params { - saveReference = true + save_reference = true max_memory = 125.GB max_cpus = 16