From fbe7bd133ab06a7d0ce0ecc28be4688586e8aaea Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 25 Sep 2020 08:33:53 +0200 Subject: [PATCH 1/4] update uppmax specific sarek config --- conf/pipeline/sarek/uppmax.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config index df2f3a2..c5aa2b0 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -4,18 +4,18 @@ 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 } if (hostname ==~ "i.*") { - params.singleCPUmem = 15.GB + params.single_cpu_mem = 15.GB } From 81f910cc95d2f9eb2d93418c6e12ffc7b46539d4 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 25 Sep 2020 09:49:43 +0200 Subject: [PATCH 2/4] add specific BamQC config --- conf/pipeline/sarek/uppmax.config | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config index c5aa2b0..694515c 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -14,6 +14,13 @@ def hostname = "hostname".execute().text.trim() if (hostname ==~ "r.*") { params.single_cpu_mem = 6400.MB + process { + withName:BamQC { + cpus = {params.max_cpus} + memory = {params.max_memory} + } + } + } if (hostname ==~ "i.*") { From 8c0cc4b9ec2e2d24fc4b11a63f2303a3e5277786 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 25 Sep 2020 09:57:50 +0200 Subject: [PATCH 3/4] code polishing --- 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 694515c..46d95a5 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -14,13 +14,13 @@ def hostname = "hostname".execute().text.trim() if (hostname ==~ "r.*") { params.single_cpu_mem = 6400.MB + process { withName:BamQC { cpus = {params.max_cpus} memory = {params.max_memory} } } - } if (hostname ==~ "i.*") { From 2ccbdd3367d62866ca25720984eb51eebb19bde8 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Mon, 28 Sep 2020 13:59:42 +0200 Subject: [PATCH 4/4] update params to latest version --- conf/uppmax.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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