From eacdf89e534acd9db3837057f9439875fa3079df Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 20 Apr 2021 13:17:35 +0200 Subject: [PATCH 1/2] Update eva.config --- conf/pipeline/eager/eva.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 2e07d57..fa7667d 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -61,7 +61,7 @@ process { // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use withName: makeSeqDict { - clusterOptions = { "-S /bin/bash -v JAVA_OPTS='-XX:ParallelGCThreads=1' -l h_vmem=${(task.memory.toGiga() + 3)}G,virtual_free=${(task.memory.toGiga() + 3)}G" } + clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: fastqc { @@ -212,4 +212,4 @@ profiles { bwaalnl = 16500 } } -} \ No newline at end of file +} From 3bcd55966df5720f7fc9beef80ac282c62b2b359 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 5 May 2021 11:39:33 +0200 Subject: [PATCH 2/2] Update eva.config --- conf/pipeline/eager/eva.config | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index fa7667d..0b7bbae 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -79,6 +79,10 @@ process { withName: markduplicates { clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" } } + + withName: library_merge { + clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" } + } withName: malt { clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }