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tasks/samtools.wdl
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| 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 5000000000 ${bam} -o ${sorted_bam} | |||||
| /opt/conda/bin/samtools sort -m 500000000 ${bam} -o ${sorted_bam} | |||||
| /opt/conda/bin/samtools index ${sorted_bam} | /opt/conda/bin/samtools index ${sorted_bam} | ||||
| >>> | >>> | ||||
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