diff --git a/conf/modules.config b/conf/modules.config index 917f26c0..3cbb23bb 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -138,10 +138,13 @@ process { } withName: "^.*CRAM_CALL_GENOTYPE_GATK4:CRAM_CALL_GATK4:GATK4_HAPLOTYPECALLER\$" { - time = { 16.h * task.attempt } + cpus = { 8 * task.attempt } + memory = { 8.GB * task.attempt } + time = { 16.h * task.attempt } ext.prefix = {"${meta.id}.g"} ext.args = { [ + "--native-pair-hmm-threads ${task.cpus}", '-ERC GVCF -contamination "0"', '-GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90', '-G StandardAnnotation -G StandardHCAnnotation -G AS_StandardAnnotation',