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Code Issues Releases Packages Activity

rm unnecessary spark_user

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SusiJo 2022-05-25 16:38:48 +02:00
parent 1400f2e683
commit b34e5ea6bf
1 changed files with 1 additions and 1 deletions
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modules/gatk4/markduplicatesspark/main.nf
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@ -25,6 +25,7 @@ process GATK4_MARKDUPLICATES_SPARK {
prefix = task.ext.prefix ?: "${meta.id}" prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"--input $it"}.join(' ') def input_list = bam.collect{"--input $it"}.join(' ')
def avail_mem = 3 def avail_mem = 3
if (!task.memory) { if (!task.memory) {
log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@ -32,7 +33,6 @@ process GATK4_MARKDUPLICATES_SPARK {
avail_mem = task.memory.giga avail_mem = task.memory.giga
} }
""" """
export SPARK_USER=spark3
gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\ gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
$input_list \\ $input_list \\