From adeec6422f4344135d87e259650b8315b31b012d Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Tue, 13 Feb 2024 16:41:03 +0100
Subject: [PATCH] fix cpu usage from hicstuff functions
---
modules/local/hicstuff/cutsite.nf | 2 +-
modules/local/hicstuff/iteralign.nf | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/local/hicstuff/cutsite.nf b/modules/local/hicstuff/cutsite.nf
index acba59a..161eed1 100644
--- a/modules/local/hicstuff/cutsite.nf
+++ b/modules/local/hicstuff/cutsite.nf
@@ -19,7 +19,7 @@ process CUTSITE {
def output_rev = task.ext.output_rev ?: "${meta2.id}_${meta2.chunk}_${meta2.mates}.fastq"
"""
- hicstuff_cutsite.py -r1 ${reads1} -r2 ${reads2} -e ${digestion} -o1 ${output_for} -o2 ${output_rev} ${args}
+ hicstuff_cutsite.py -r1 ${reads1} -r2 ${reads2} -e ${digestion} -o1 ${output_for} -o2 ${output_rev} -c ${task.cpus} ${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
hicstuff: v3.1.3)
diff --git a/modules/local/hicstuff/iteralign.nf b/modules/local/hicstuff/iteralign.nf
index 82ad24a..d455a7c 100644
--- a/modules/local/hicstuff/iteralign.nf
+++ b/modules/local/hicstuff/iteralign.nf
@@ -22,7 +22,7 @@ process ITERALIGN {
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"`
[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
- hicstuff_iteralign.py -r ${reads} -g \$INDEX -b ${prefix}.bam ${args}
+ hicstuff_iteralign.py -r ${reads} -g \$INDEX -b ${prefix}.bam -n ${task.cpus} ${args}
samtools view -F 2048 -h -@ $task.cpus -O BAM ${prefix}.bam -o ${prefix}_iteraligned.bam
--
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