diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf index 77e135db..8265e16f 100644 --- a/modules/gatk4/markduplicatesspark/main.nf +++ b/modules/gatk4/markduplicatesspark/main.nf @@ -25,6 +25,7 @@ process GATK4_MARKDUPLICATES_SPARK { prefix = task.ext.prefix ?: "${meta.id}" def input_list = bam.collect{"--input $it"}.join(' ') + def avail_mem = 3 if (!task.memory) { log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' @@ -32,7 +33,6 @@ process GATK4_MARKDUPLICATES_SPARK { avail_mem = task.memory.giga } """ - export SPARK_USER=spark3 gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\ $input_list \\