From 9b451b53b7a539c98cf91d25642792318146b0c2 Mon Sep 17 00:00:00 2001 From: lquayle88 Date: Sat, 1 Oct 2022 23:31:51 +0100 Subject: [PATCH] Increased cpus and memory for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek --- conf/pipeline/sarek/sbc_sharc.config | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/conf/pipeline/sarek/sbc_sharc.config b/conf/pipeline/sarek/sbc_sharc.config index 570284d..170b8bd 100644 --- a/conf/pipeline/sarek/sbc_sharc.config +++ b/conf/pipeline/sarek/sbc_sharc.config @@ -26,13 +26,13 @@ process { withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } } withLabel:process_medium { cpus = { check_max( 6 * task.attempt, 'cpus' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } + time = { check_max( 8.h * task.attempt, 'time' ) } } withLabel:process_high { @@ -75,7 +75,8 @@ process { } withName:'GATK4_MARKDUPLICATES' { - memory = { check_max( 20.GB * task.attempt, 'memory' ) } + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 30.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } }