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Set BWA and bwamem2 index memory dynamically #6628

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Set BWA and bwamem2 index memory dynamically #6628

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9c0b700
fix: Update bwamem2 to use 28.B of memory per byte of fasta
edmundmiller Sep 11, 2024
f10c3f8
chore: Set expected memory for bwa index
edmundmiller Sep 11, 2024
75343d0
fix: Round up to 6.B because 5.5.B breaks parser
edmundmiller Sep 11, 2024
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4 changes: 3 additions & 1 deletion modules/nf-core/bwa/index/main.nf
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
process BWA_INDEX {
tag "$fasta"
label 'process_single'
// NOTE requires 5.37N memory where N is the size of the database
// source: https://bio-bwa.sourceforge.net/bwa.shtml#8
memory { 6.B * fasta.size() }

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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4 changes: 3 additions & 1 deletion modules/nf-core/bwamem2/index/main.nf
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
process BWAMEM2_INDEX {
tag "$fasta"
label 'process_single'
// NOTE Requires 28N GB memory where N is the size of the reference sequence
// source: https://github.com/bwa-mem2/bwa-mem2/issues/9
memory { 28.B * fasta.size() }

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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