From f187f8a101311dfd41e1895500d524267a87a10f Mon Sep 17 00:00:00 2001
From: Emilio Palumbo <emiliopalumbo@gmail.com>
Date: Thu, 20 Jul 2023 10:40:12 +0200
Subject: [PATCH] Reduce memory usage in RSEM quantification process

---
 grape-pipeline.nf                                    | 2 ++
 templates/quantification/RSEM-Paired-End-MATE1_SENSE | 4 ++--
 templates/quantification/RSEM-Paired-End-MATE2_SENSE | 4 ++--
 templates/quantification/RSEM-Paired-End-NONE        | 4 ++--
 templates/quantification/RSEM-Single-End-ANTISENSE   | 4 ++--
 templates/quantification/RSEM-Single-End-NONE        | 4 ++--
 templates/quantification/RSEM-Single-End-SENSE       | 4 ++--
 7 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/grape-pipeline.nf b/grape-pipeline.nf
index 7f49be7..6cde7d7 100755
--- a/grape-pipeline.nf
+++ b/grape-pipeline.nf
@@ -736,6 +736,8 @@ process quantification {
     viewTx = "TranscriptQuantifications"
     viewGn = "GeneQuantifications"
     memory = (task.memory ?: 1.GB).toMega()
+    sortMemory = Math.max(1024, (memory / 2) as long)
+    ciMemory = Math.max(1024, (memory / 4) as long)
     command = "${task.process}/${params.quantificationTool}"
     if ( params.quantificationTool == 'RSEM') {
         command += "-${pairedEnd ? 'Paired-End' : 'Single-End'}"
diff --git a/templates/quantification/RSEM-Paired-End-MATE1_SENSE b/templates/quantification/RSEM-Paired-End-MATE1_SENSE
index de1b23d..b0fb871 100644
--- a/templates/quantification/RSEM-Paired-End-MATE1_SENSE
+++ b/templates/quantification/RSEM-Paired-End-MATE1_SENSE
@@ -2,14 +2,14 @@
 set -e
 set -u
 
-sambamba sort -t ${cpus} -m ${memory}MB -N -M -l 0 -o - ${bam} \
+sambamba sort -t ${cpus} -m ${sortMemory}MB -N -M -l 0 -o - ${bam} \
   | rsem-calculate-expression --bam \
                           --estimate-rspd  \
                           --calc-ci \
                           --no-bam-output \
                           --seed 12345 \
                           -p ${cpus} \
-                          --ci-memory ${memory} \
+                          --ci-memory ${ciMemory} \
                           --paired-end \
                           --forward-prob 1 \
                           - \
diff --git a/templates/quantification/RSEM-Paired-End-MATE2_SENSE b/templates/quantification/RSEM-Paired-End-MATE2_SENSE
index 7ad59a6..9eb43e7 100644
--- a/templates/quantification/RSEM-Paired-End-MATE2_SENSE
+++ b/templates/quantification/RSEM-Paired-End-MATE2_SENSE
@@ -2,14 +2,14 @@
 set -e
 set -u
 
-sambamba sort -t ${cpus} -m ${memory}MB -N -M -l 0 -o - ${bam} \
+sambamba sort -t ${cpus} -m ${sortMemory}MB -N -M -l 0 -o - ${bam} \
   | rsem-calculate-expression --bam \
                           --estimate-rspd  \
                           --calc-ci \
                           --no-bam-output \
                           --seed 12345 \
                           -p ${cpus} \
-                          --ci-memory ${memory} \
+                          --ci-memory ${ciMemory} \
                           --paired-end \
                           --forward-prob 0 \
                           - \
diff --git a/templates/quantification/RSEM-Paired-End-NONE b/templates/quantification/RSEM-Paired-End-NONE
index 771ce64..2557930 100644
--- a/templates/quantification/RSEM-Paired-End-NONE
+++ b/templates/quantification/RSEM-Paired-End-NONE
@@ -2,14 +2,14 @@
 set -e
 set -u
 
-sambamba sort -t ${cpus} -m ${memory}MB -N -M -l 0 -o - ${bam} \
+sambamba sort -t ${cpus} -m ${sortMemory}MB -N -M -l 0 -o - ${bam} \
   | rsem-calculate-expression --bam \
                           --estimate-rspd  \
                           --calc-ci \
                           --no-bam-output \
                           --seed 12345 \
                           -p ${cpus} \
-                          --ci-memory ${memory} \
+                          --ci-memory ${ciMemory} \
                           --paired-end \
                           - \
                           ${quantRef}/RSEMref \
diff --git a/templates/quantification/RSEM-Single-End-ANTISENSE b/templates/quantification/RSEM-Single-End-ANTISENSE
index 3f25653..0b45f80 100644
--- a/templates/quantification/RSEM-Single-End-ANTISENSE
+++ b/templates/quantification/RSEM-Single-End-ANTISENSE
@@ -2,14 +2,14 @@
 set -e
 set -u
 
-sambamba sort -t ${cpus} -m ${memory}MB -N -l 0 -o - ${bam} \
+sambamba sort -t ${cpus} -m ${sortMemory}MB -N -l 0 -o - ${bam} \
   | rsem-calculate-expression --bam \
                           --estimate-rspd  \
                           --calc-ci \
                           --no-bam-output \
                           --seed 12345 \
                           -p ${cpus} \
-                          --ci-memory ${memory} \
+                          --ci-memory ${ciMemory} \
                           --forward-prob 0 \
                           - \
                           ${quantRef}/RSEMref \
diff --git a/templates/quantification/RSEM-Single-End-NONE b/templates/quantification/RSEM-Single-End-NONE
index e50fb1f..237c361 100644
--- a/templates/quantification/RSEM-Single-End-NONE
+++ b/templates/quantification/RSEM-Single-End-NONE
@@ -2,14 +2,14 @@
 set -e
 set -u
 
-sambamba sort -t ${cpus} -m ${memory}MB -N -l 0 -o - ${bam} \
+sambamba sort -t ${cpus} -m ${sortMemory}MB -N -l 0 -o - ${bam} \
   | rsem-calculate-expression --bam \
                           --estimate-rspd  \
                           --calc-ci \
                           --no-bam-output \
                           --seed 12345 \
                           -p ${cpus} \
-                          --ci-memory ${memory} \
+                          --ci-memory ${ciMemory} \
                           - \
                           ${quantRef}/RSEMref \
                           ${prefix}
diff --git a/templates/quantification/RSEM-Single-End-SENSE b/templates/quantification/RSEM-Single-End-SENSE
index a6aa406..68e0547 100644
--- a/templates/quantification/RSEM-Single-End-SENSE
+++ b/templates/quantification/RSEM-Single-End-SENSE
@@ -2,14 +2,14 @@
 set -e
 set -u
 
-sambamba sort -t ${cpus} -m ${memory}MB -N -l 0 -o - ${bam} \
+sambamba sort -t ${cpus} -m ${sortMemory}MB -N -l 0 -o - ${bam} \
   | rsem-calculate-expression --bam \
                           --estimate-rspd  \
                           --calc-ci \
                           --no-bam-output \
                           --seed 12345 \
                           -p ${cpus} \
-                          --ci-memory ${memory} \
+                          --ci-memory ${ciMemory} \
                           --forward-prob 1 \
                           - \
                           ${quantRef}/RSEMref \