From 670135406080fed543aa42d2eb428305dde02042 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 20 Aug 2021 10:11:11 +0200 Subject: [PATCH] Add genotyping_ug to SGE fixes --- conf/pipeline/eager/eva.config | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 16e185a..880df27 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -124,6 +124,10 @@ process { clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } + + withName: genotyping_ug { + clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + } } @@ -259,6 +263,10 @@ profiles { withName: circulargenerator { clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } + + withName: genotyping_ug { + clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + } withName: preseq { clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } @@ -398,7 +406,11 @@ profiles { withName: circulargenerator { clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } - + + withName: genotyping_ug { + clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + } + withName: preseq { clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }