From ab8998e12bd3739d060e52cedd50ab92e9b7bf16 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 27 Feb 2020 16:52:51 +0100 Subject: [PATCH 1/5] Update uppmax.config --- conf/pipeline/sarek/uppmax.config | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config index 2096684..84b65f8 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -3,10 +3,12 @@ params { config_profile_contact = 'Maxime Garcia (@MaxUlysse)' config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs' -} -params { - // Just useful until iGenomes is updated on UPPMAX +// Just useful until iGenomes is updated on UPPMAX igenomeIgnore = true genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle' } + +if (hostname ==~ "i.*") { + params.singleCPUmem = 15.GB +} From 17d6a7e922eca8170ae21c1aa80d483312270338 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 27 Feb 2020 17:02:13 +0100 Subject: [PATCH 2/5] Update conf/pipeline/sarek/uppmax.config --- conf/pipeline/sarek/uppmax.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config index 84b65f8..dc3a86a 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -4,6 +4,7 @@ params { config_profile_contact = 'Maxime Garcia (@MaxUlysse)' config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs' + singleCPUmem = 7.GB // Just useful until iGenomes is updated on UPPMAX igenomeIgnore = true genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle' From 09ff8f5790819b80aece23d135f5169d007ab967 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 27 Feb 2020 17:02:31 +0100 Subject: [PATCH 3/5] Update conf/pipeline/sarek/uppmax.config --- conf/pipeline/sarek/uppmax.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config index dc3a86a..56878b6 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -4,7 +4,7 @@ params { config_profile_contact = 'Maxime Garcia (@MaxUlysse)' config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs' - singleCPUmem = 7.GB + singleCPUmem = 7.GB // Just useful until iGenomes is updated on UPPMAX igenomeIgnore = true genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle' From 8acbdacf0331f6fd61dfa7db822783c45e5d4014 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 27 Feb 2020 17:21:03 +0100 Subject: [PATCH 4/5] Update conf/pipeline/sarek/uppmax.config Co-Authored-By: Johannes Alneberg --- conf/pipeline/sarek/uppmax.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config index 56878b6..78955bf 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -4,7 +4,7 @@ params { config_profile_contact = 'Maxime Garcia (@MaxUlysse)' config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs' - singleCPUmem = 7.GB + singleCPUmem = 7000.MB // Just useful until iGenomes is updated on UPPMAX igenomeIgnore = true genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle' From 9a8bb12020acd5eb5fdaa6b48426df7d3620ba21 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 27 Feb 2020 17:22:03 +0100 Subject: [PATCH 5/5] Update conf/pipeline/sarek/uppmax.config --- conf/pipeline/sarek/uppmax.config | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config index 78955bf..1e467dd 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -9,7 +9,9 @@ params { igenomeIgnore = true genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle' } - + if (hostname ==~ "r.*") { + params.singleCPUmem = 6400.MB +} if (hostname ==~ "i.*") { params.singleCPUmem = 15.GB }