diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 5eebacefeb3550d6dbb8c25717e48236c2b61ddb..f4d54ebab9bbacf91da9e42f0f884905d7407937 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -1452,7 +1452,7 @@ process alignData { # sort the bam file using Samtools echo -e "LOG: sorting the bam file" >> ${repRID}.align.log mem=\$(vmstat -s -S K | grep 'total memory' | grep -o '[0-9]*') - mem=\$(expr \${mem} / `nproc` \* 85 / 100) + mem=\$(expr \${mem} / `nproc` \\* 85 / 100) samtools sort -@ `nproc` -m \${mem}K -O BAM -o ${repRID}.sorted.bam ${repRID}.bam # index the sorted bam using Samtools