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Fastqc: FIX memory over-allocation #6156

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merged 3 commits into from
Aug 22, 2024
Merged

Fastqc: FIX memory over-allocation #6156

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07fa9d8
FIX memory over-allocation
sguizard Aug 9, 2024
8c09ed2
Comment to explain why dividing by task.cpu
sguizard Aug 13, 2024
9d14446
Merge branch 'master' into fastqc_mem_overallocation
sguizard Aug 13, 2024
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5 changes: 4 additions & 1 deletion modules/nf-core/fastqc/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,10 @@ process FASTQC {
def rename_to = old_new_pairs*.join(' ').join(' ')
def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')

def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
// The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
// https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
// Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
// FastQC memory value allowed range (100 - 10000)
def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)

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2 changes: 1 addition & 1 deletion subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap
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Expand Up @@ -521,4 +521,4 @@
},
"timestamp": "2024-07-22T17:06:09.844235"
}
}
}
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