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Update HaplotypeCaller_GATK4_VCF to use MEM_SIZE and MEM_UNIT #1448

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Update HaplotypeCaller_GATK4_VCF to use MEM_SIZE and MEM_UNIT #1448

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11 changes: 8 additions & 3 deletions tasks/broad/GermlineVariantDiscovery.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -124,9 +124,14 @@ task HaplotypeCaller_GATK4_VCF {
# We need at least 1 GB of available memory outside of the Java heap in order to execute native code, thus, limit
# Java's memory by the total memory minus 1 GB. We need to compute the total memory as it might differ from
# memory_size_gb because of Cromwell's retry with more memory feature.
# Note: In the future this should be done using Cromwell's ${MEM_SIZE} and ${MEM_UNIT} environment variables,
# which do not rely on the output format of the `free` command.
available_memory_mb=$(free -m | awk '/^Mem/ {print $2}')
mem_unit=$(echo "${MEM_UNIT:-}" | cut -c 1)
if [[ $mem_unit == "M" ]]; then
available_memory_mb=$(awk "BEGIN {print int($MEM_SIZE)}")
elif [[ $mem_unit == "G" ]]; then
available_memory_mb=$(awk "BEGIN {print int($MEM_SIZE * 1024)}")
else
available_memory_mb=$(free -m | awk '/^Mem/ {print $2}')
fi
let java_memory_size_mb=available_memory_mb-1024
echo Total available memory: ${available_memory_mb} MB >&2
echo Memory reserved for Java: ${java_memory_size_mb} MB >&2
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