From 78fd89082baf553264127853a5bab2d85229e0e9 Mon Sep 17 00:00:00 2001
From: Emilio Palumbo <emiliopalumbo@gmail.com>
Date: Thu, 20 Jul 2023 14:58:23 +0200
Subject: [PATCH] Reduce memory usage in RSEM quantification process
---
modules/quantification/rsem/main.nf | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/modules/quantification/rsem/main.nf b/modules/quantification/rsem/main.nf
index 9e43e69..24c5d43 100644
--- a/modules/quantification/rsem/main.nf
+++ b/modules/quantification/rsem/main.nf
@@ -61,6 +61,8 @@ process quantify {
viewTx = "TranscriptQuantifications"
viewGn = "GeneQuantifications"
def memory = (task.memory ?: 1.GB).toMega()
+ def sortMemFrac = params.rsemSkipCi ? 0.75 : 0.5
+ def sortMemory = Math.max(1024, (memory * sortMemFrac) as long)
def forwardProb = null
switch (readStrand) {
@@ -73,7 +75,7 @@ process quantify {
}
def cmd = []
- cmd << "sambamba sort -t ${task.cpus} -m ${memory}MB -N -M -l 0 -o - ${bam} \\"
+ cmd << "sambamba sort -t ${task.cpus} -m ${sortMemory}MB -N -M -l 0 -o - ${bam} \\"
cmd << """\
| rsem-calculate-expression -p ${task.cpus} \\
--bam \\
@@ -89,9 +91,10 @@ process quantify {
--forward-prob ${forwardProb} \\"""
}
if ( ! params.rsemSkipCi ) {
+ def ciMemory = Math.max(1024, (memory / 4) as long)
cmd << """\
--calc-ci \\
- --ci-memory ${memory} \\"""
+ --ci-memory ${ciMemory} \\"""
}
cmd << """\
- \\