From 0bfa5ba95d545bd097152ab505d10bcb4ca9da5c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 18 Jan 2021 21:28:20 -0600
Subject: [PATCH] Copy samtools mem param fix to align sample
---
workflow/rna-seq.nf | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index f4d54eb..23d59c8 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -757,10 +757,12 @@ process alignSampleData {
# convert the output sam file to a sorted bam file using Samtools
echo -e "LOG: converting from sam to bam" >> ${repRID}.${ref}.alignSampleData.log
- samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${ref}.sampled.bam ${ref}.sampled.sam
+ samtools view -1 -@ `nproc` -m \${mem}K -F 4 -F 8 -F 256 -o ${ref}.sampled.bam ${ref}.sampled.sam
# sort the bam file using Samtools
echo -e "LOG: sorting the bam file" >> ${repRID}.${ref}.alignSampleData.log
+ mem=\$(vmstat -s -S K | grep 'total memory' | grep -o '[0-9]*')
+ mem=\$(expr \${mem} / `nproc` \\* 85 / 100)
samtools sort -@ `nproc` -O BAM -o ${ref}.sampled.sorted.bam ${ref}.sampled.bam
# index the sorted bam using Samtools
--
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