From 2a0b4e0f678f18567eb9dbeb12d7c698a43b37a1 Mon Sep 17 00:00:00 2001
From: Xavier Grand <xavier.grand@ens-lyon.fr>
Date: Mon, 5 Dec 2022 15:09:22 +0100
Subject: [PATCH] src/nf_modules/star/main_2.7.8a.nf take into account
available memory to limit file compression ressource.
---
src/nf_modules/star/main_2.7.8a.nf | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf
index d865c75..389a2ee 100644
--- a/src/nf_modules/star/main_2.7.8a.nf
+++ b/src/nf_modules/star/main_2.7.8a.nf
@@ -34,6 +34,7 @@ process index_with_gtf {
tuple val(genome_id), path ("*"), emit: index
script:
+ memory = "${task.memory}" - ~/\s*GB/
"""
STAR --runThreadN ${task.cpus} --runMode genomeGenerate \
--genomeDir ./ \
@@ -250,6 +251,7 @@ process mapping2fusion {
tuple val(reads_id), path("*.bam"), emit: bam
script:
+ memory = "${task.memory}" - ~/\s*GB/
if (reads_id instanceof List){
file_prefix = reads_id[0]
} else {
@@ -281,7 +283,8 @@ STAR --runThreadN ${task.cpus} \
--chimScoreJunctionNonGTAG 0 \
--chimScoreSeparation 1 \
--chimSegmentReadGapMax 3 \
---chimMultimapNmax 50
+--chimMultimapNmax 50 \
+--limitBAMsortRAM ${memory}000000000
mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam
"""
@@ -311,7 +314,8 @@ STAR --runThreadN ${task.cpus} \
--chimScoreJunctionNonGTAG 0 \
--chimScoreSeparation 1 \
--chimSegmentReadGapMax 3 \
---chimMultimapNmax 50
+--chimMultimapNmax 50 \
+--limitBAMsortRAM ${memory}000000000
mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam
"""
--
GitLab