From a22602f4480ede2f6f9884a6286aae4f00df08f6 Mon Sep 17 00:00:00 2001 From: jemten Date: Fri, 1 Dec 2023 10:08:36 +0100 Subject: [PATCH 1/2] temp fix of mem allocation for gatk cnv --- modules.json | 6 ++++-- .../germlinecnvcaller/gatk4-germlinecnvcaller.diff | 14 ++++++++++++++ modules/nf-core/gatk4/germlinecnvcaller/main.nf | 2 +- .../gatk4-postprocessgermlinecnvcalls.diff | 14 ++++++++++++++ .../gatk4/postprocessgermlinecnvcalls/main.nf | 2 +- 5 files changed, 34 insertions(+), 4 deletions(-) create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/gatk4-germlinecnvcaller.diff create mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/gatk4-postprocessgermlinecnvcalls.diff diff --git a/modules.json b/modules.json index e45a6fd8..1c4709dd 100644 --- a/modules.json +++ b/modules.json @@ -153,7 +153,8 @@ "gatk4/germlinecnvcaller": { "branch": "master", "git_sha": "8c4542e5d421c4690cf1fa6ec729e9304763fdaf", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/gatk4/germlinecnvcaller/gatk4-germlinecnvcaller.diff" }, "gatk4/intervallisttools": { "branch": "master", @@ -178,7 +179,8 @@ "gatk4/postprocessgermlinecnvcalls": { "branch": "master", "git_sha": "8c4542e5d421c4690cf1fa6ec729e9304763fdaf", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/gatk4/postprocessgermlinecnvcalls/gatk4-postprocessgermlinecnvcalls.diff" }, "gatk4/preprocessintervals": { "branch": "master", diff --git a/modules/nf-core/gatk4/germlinecnvcaller/gatk4-germlinecnvcaller.diff b/modules/nf-core/gatk4/germlinecnvcaller/gatk4-germlinecnvcaller.diff new file mode 100644 index 00000000..c501e50e --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/gatk4-germlinecnvcaller.diff @@ -0,0 +1,14 @@ +Changes in module 'nf-core/gatk4/germlinecnvcaller' +--- modules/nf-core/gatk4/germlinecnvcaller/main.nf ++++ modules/nf-core/gatk4/germlinecnvcaller/main.nf +@@ -36,7 +36,7 @@ + avail_mem = (task.memory.mega*0.8).intValue() + } + """ +- gatk --java-options "-Xmx${avail_mem}g" GermlineCNVCaller \\ ++ gatk --java-options "-Xmx${avail_mem}M" GermlineCNVCaller \\ + $input_list \\ + $ploidy_command \\ + $output_command \\ + +************************************************************ diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index 973a0d3b..441e730f 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -36,7 +36,7 @@ process GATK4_GERMLINECNVCALLER { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" GermlineCNVCaller \\ + gatk --java-options "-Xmx${avail_mem}M" GermlineCNVCaller \\ $input_list \\ $ploidy_command \\ $output_command \\ diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/gatk4-postprocessgermlinecnvcalls.diff b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/gatk4-postprocessgermlinecnvcalls.diff new file mode 100644 index 00000000..b922c53d --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/gatk4-postprocessgermlinecnvcalls.diff @@ -0,0 +1,14 @@ +Changes in module 'nf-core/gatk4/postprocessgermlinecnvcalls' +--- modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf ++++ modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +@@ -35,7 +35,7 @@ + avail_mem = (task.memory.mega*0.8).intValue() + } + """ +- gatk --java-options "-Xmx${avail_mem}g" PostprocessGermlineCNVCalls \\ ++ gatk --java-options "-Xmx${avail_mem}M" PostprocessGermlineCNVCalls \\ + $calls_command \\ + $model_command \\ + $ploidy_command \\ + +************************************************************ diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index d6223043..d916c2af 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -35,7 +35,7 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" PostprocessGermlineCNVCalls \\ + gatk --java-options "-Xmx${avail_mem}M" PostprocessGermlineCNVCalls \\ $calls_command \\ $model_command \\ $ploidy_command \\ From 0d2a770ce7044f207228dd3fc525e6d8d9c8b388 Mon Sep 17 00:00:00 2001 From: jemten Date: Fri, 1 Dec 2023 10:14:34 +0100 Subject: [PATCH 2/2] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 90aec003..de991758 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -46,6 +46,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixes vep starting as many instances as the square of the number of scatters. [#405](https://github.com/nf-core/raredisease/pull/405) - Replaced the logic where we added an arbitrary substring to keep file names unique after alignment which we then removed using a split operator, with a simple copy operation. [#425](https://github.com/nf-core/raredisease/pull/425/files) - Preventing a crash of rhocall annotate in the case of running four individuals whereof two are affected. +- Fixed memory qualifier in gatk4 germlinecnvcaller and postprocessgermlinecnvcalls ### `Updated`