set -o pipefail | set -o pipefail | ||||
set -e | set -e | ||||
/opt/conda/bin/samtools view -bS ${sam} > ${bam} | /opt/conda/bin/samtools view -bS ${sam} > ${bam} | ||||
/opt/conda/bin/samtools sort -m 500000000 ${bam} -o ${sorted_bam} | |||||
/opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam} | |||||
/opt/conda/bin/samtools index ${sorted_bam} | /opt/conda/bin/samtools index ${sorted_bam} | ||||
>>> | >>> | ||||