From 527d9358b9475d55cfdc04d0e8ebf72abd6f9d5f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 18 Jan 2021 21:38:31 -0600
Subject: [PATCH] Move mem param to sort
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 23d59c8..abec019 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -757,13 +757,13 @@ 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` -m \${mem}K -F 4 -F 8 -F 256 -o ${ref}.sampled.bam ${ref}.sampled.sam
+ samtools view -1 -@ `nproc` -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
+ samtools sort -@ `nproc` -m \${mem}K -O BAM -o ${ref}.sampled.sorted.bam ${ref}.sampled.bam
# index the sorted bam using Samtools
echo -e "LOG: indexing sorted bam file" >> ${repRID}.${ref}.alignSampleData.log
--
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