Wrong memory qualifier in postprocessgermlinecnvcalls

[Jakob37]

Description of the bug

In GATK4_POSTPROCESSGERMLINECNVCALLS, the memory is handled in megabytes, but assigned to the java process in gigabytes.

See: https://github.com/nf-core/raredisease/blob/master/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf

If for instance having access to 20GB, this would lead to the java being told to run with 20TB.

Key parts from the script block.

def avail_mem = 3072 <- Megabytes
if (!task.memory) {
    log.info '[GATK GermlineCNVCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
    avail_mem = (task.memory.mega*0.8).intValue() <- Megabytes
}
"""
gatk --java-options "-Xmx${avail_mem}g" PostprocessGermlineCNVCalls \\ <- Assigned in gigabytes
    $calls_command \\
    $model_command \\
    $ploidy_command \\
    --output-genotyped-intervals ${prefix}_genotyped_intervals.vcf.gz \\
    --output-genotyped-segments ${prefix}_genotyped_segments.vcf.gz \\
    --output-denoised-copy-ratios ${prefix}_denoised.vcf.gz
"""

Command used and terminal output

No response

Relevant files

No response

System information

No response

[jemten]

That's a lot of memory 😅