Reduce memory usage in RSEM quantification process

guigolab · Jul 20, 2023 · f187f8a · f187f8a
1 parent ae1ecc6
commit f187f8a
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Showing 7 changed files with 14 additions and 12 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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 \